Starting phenix.real_space_refine on Mon Jan 20 09:23:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9v_19013/01_2025/8r9v_19013.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 4 5.21 5 S 98 5.16 5 C 9407 2.51 5 N 2516 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14851 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 6000 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 26, 'TRANS': 713} Chain breaks: 1 Chain: "B" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2936 Unusual residues: {'ACE': 1} Classifications: {'peptide': 375, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.09, per 1000 atoms: 0.61 Number of scatterers: 14851 At special positions: 0 Unit cell: (110.21, 169.06, 140.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 9 15.00 Mg 4 11.99 O 2817 8.00 N 2516 7.00 C 9407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM14792 O5' ADP B 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.6 seconds 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 25 sheets defined 49.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 154 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.946A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.132A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.224A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.650A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 392 through 423 Processing helix chain 'A' and resid 448 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 493 through 501 removed outlier: 4.789A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.714A pdb=" N LEU A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.779A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 593 removed outlier: 3.981A pdb=" N GLU A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 673 through 685 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 711 through 714 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.813A pdb=" N LYS A 733 " --> pdb=" O ASN A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 753 through 774 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 129 removed outlier: 3.511A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 218 removed outlier: 3.871A pdb=" N ILE B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.812A pdb=" N CYS B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 262 through 263 No H-bonds generated for 'chain 'B' and resid 262 through 263' Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.565A pdb=" N LYS B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.568A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.715A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 338 through 349 removed outlier: 3.702A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 375 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.610A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.510A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.763A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.185A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.502A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 375 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.945A pdb=" N HIS A 61 " --> pdb=" O TRP A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.615A pdb=" N LEU A 107 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 661 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 109 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A 158 " --> pdb=" O HIS A 656 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 658 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE A 160 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS A 660 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A 162 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 161 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 435 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 221 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR A 241 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 223 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N MET A 239 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU A 225 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 237 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A 227 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 699 through 702 Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.536A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.436A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER B 301 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 154 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 298 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.861A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.468A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.920A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.480A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 238 through 241 730 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2896 1.33 - 1.45: 3589 1.45 - 1.58: 8515 1.58 - 1.70: 12 1.70 - 1.82: 165 Bond restraints: 15177 Sorted by residual: bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP A 903 " pdb=" C5 ADP A 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O1 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.565 1.465 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 15172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 16900 2.24 - 4.48: 3393 4.48 - 6.73: 213 6.73 - 8.97: 20 8.97 - 11.21: 21 Bond angle restraints: 20547 Sorted by residual: angle pdb=" C ALA A 217 " pdb=" N SER A 218 " pdb=" CA SER A 218 " ideal model delta sigma weight residual 122.26 133.02 -10.76 1.60e+00 3.91e-01 4.53e+01 angle pdb=" CA GLN C 263 " pdb=" C GLN C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 117.73 123.65 -5.92 1.04e+00 9.25e-01 3.24e+01 angle pdb=" N PRO A 655 " pdb=" CA PRO A 655 " pdb=" C PRO A 655 " ideal model delta sigma weight residual 111.68 120.90 -9.22 1.67e+00 3.59e-01 3.05e+01 angle pdb=" O PRO B 333 " pdb=" C PRO B 333 " pdb=" N PRO B 334 " ideal model delta sigma weight residual 121.15 118.68 2.47 4.70e-01 4.53e+00 2.75e+01 angle pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N SER A 165 " ideal model delta sigma weight residual 115.36 122.48 -7.12 1.37e+00 5.33e-01 2.70e+01 ... (remaining 20542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.15: 8897 33.15 - 66.29: 210 66.29 - 99.44: 33 99.44 - 132.59: 2 132.59 - 165.74: 6 Dihedral angle restraints: 9148 sinusoidal: 3743 harmonic: 5405 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 134.26 165.74 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.90 162.10 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 92.73 -152.73 1 2.00e+01 2.50e-03 4.53e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1215 0.074 - 0.149: 756 0.149 - 0.223: 230 0.223 - 0.297: 45 0.297 - 0.371: 5 Chirality restraints: 2251 Sorted by residual: chirality pdb=" CA GLU D 334 " pdb=" N GLU D 334 " pdb=" C GLU D 334 " pdb=" CB GLU D 334 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA VAL A 686 " pdb=" N VAL A 686 " pdb=" C VAL A 686 " pdb=" CB VAL A 686 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE A 15 " pdb=" N ILE A 15 " pdb=" C ILE A 15 " pdb=" CB ILE A 15 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 2248 not shown) Planarity restraints: 2631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 232 " -0.138 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR A 232 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 232 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 232 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 TYR A 232 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 232 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR A 232 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 232 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 127 " -0.146 2.00e-02 2.50e+03 7.58e-02 1.15e+02 pdb=" CG TYR A 127 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 127 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR A 127 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 127 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 127 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 127 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 523 " 0.089 2.00e-02 2.50e+03 5.90e-02 8.69e+01 pdb=" CG TRP A 523 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 523 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 523 " -0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP A 523 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP A 523 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 523 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 523 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 523 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 523 " 0.078 2.00e-02 2.50e+03 ... (remaining 2628 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 12 2.04 - 2.75: 981 2.75 - 3.47: 21406 3.47 - 4.18: 36994 4.18 - 4.90: 62632 Nonbonded interactions: 122025 Sorted by model distance: nonbonded pdb=" NH1 ARG C 37 " pdb=" O ASP C 51 " model vdw 1.324 3.120 nonbonded pdb=" CD1 ILE A 110 " pdb=" CD1 ILE A 661 " model vdw 1.501 3.880 nonbonded pdb=" O CYS A 561 " pdb=" CD2 PHE A 564 " model vdw 1.585 3.340 nonbonded pdb=" CA PRO B 39 " pdb=" CD2 LEU B 66 " model vdw 1.687 3.890 nonbonded pdb=" OE1 GLU A 204 " pdb=" ND2 ASN A 208 " model vdw 1.741 3.120 ... (remaining 122020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 376 or resid 401 through 402)) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.010 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.110 15177 Z= 0.849 Angle : 1.693 11.212 20547 Z= 1.171 Chirality : 0.098 0.371 2251 Planarity : 0.008 0.105 2631 Dihedral : 14.893 165.735 5676 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 0.25 % Allowed : 3.58 % Favored : 96.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 1847 helix: -1.35 (0.15), residues: 820 sheet: -2.37 (0.29), residues: 241 loop : -0.67 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.006 TRP A 523 HIS 0.014 0.001 HIS A 644 PHE 0.073 0.005 PHE A 220 TYR 0.146 0.005 TYR A 127 ARG 0.011 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 814 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8427 (mp0) REVERT: A 48 LEU cc_start: 0.7789 (tp) cc_final: 0.7512 (tt) REVERT: A 87 HIS cc_start: 0.8654 (t-90) cc_final: 0.7958 (t-90) REVERT: A 94 ILE cc_start: 0.8384 (mt) cc_final: 0.7577 (tt) REVERT: A 95 ASP cc_start: 0.7884 (t0) cc_final: 0.7598 (t0) REVERT: A 97 LYS cc_start: 0.7913 (mptt) cc_final: 0.6994 (mttp) REVERT: A 103 CYS cc_start: 0.7442 (m) cc_final: 0.7206 (t) REVERT: A 113 TYR cc_start: 0.6363 (m-80) cc_final: 0.5820 (m-80) REVERT: A 121 GLU cc_start: 0.8685 (tp30) cc_final: 0.8329 (tp30) REVERT: A 138 HIS cc_start: 0.6432 (m90) cc_final: 0.5980 (m90) REVERT: A 144 GLU cc_start: 0.8406 (tp30) cc_final: 0.8195 (tt0) REVERT: A 150 MET cc_start: 0.7823 (ttp) cc_final: 0.7314 (ttp) REVERT: A 179 TYR cc_start: 0.8620 (t80) cc_final: 0.8239 (t80) REVERT: A 222 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8323 (tptp) REVERT: A 223 TYR cc_start: 0.7676 (t80) cc_final: 0.7150 (t80) REVERT: A 225 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7001 (mp0) REVERT: A 228 PHE cc_start: 0.6764 (m-80) cc_final: 0.6065 (m-80) REVERT: A 242 TYR cc_start: 0.6942 (m-80) cc_final: 0.6347 (m-80) REVERT: A 248 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7216 (tpp80) REVERT: A 259 TYR cc_start: 0.7908 (m-80) cc_final: 0.6744 (m-80) REVERT: A 260 HIS cc_start: 0.7939 (m90) cc_final: 0.7265 (m-70) REVERT: A 262 PHE cc_start: 0.8793 (m-80) cc_final: 0.8053 (m-80) REVERT: A 304 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 305 MET cc_start: 0.8451 (tpt) cc_final: 0.8162 (tpt) REVERT: A 312 CYS cc_start: 0.8415 (m) cc_final: 0.8120 (m) REVERT: A 315 LEU cc_start: 0.6682 (mt) cc_final: 0.6397 (mt) REVERT: A 364 MET cc_start: 0.7779 (mtt) cc_final: 0.7528 (mtt) REVERT: A 370 GLU cc_start: 0.8647 (tt0) cc_final: 0.8209 (tt0) REVERT: A 408 TYR cc_start: 0.8851 (t80) cc_final: 0.8010 (t80) REVERT: A 448 SER cc_start: 0.8243 (m) cc_final: 0.7612 (p) REVERT: A 450 GLU cc_start: 0.8800 (pm20) cc_final: 0.8485 (pp20) REVERT: A 451 GLN cc_start: 0.8868 (mp10) cc_final: 0.7999 (mt0) REVERT: A 453 CYS cc_start: 0.8635 (m) cc_final: 0.8410 (m) REVERT: A 458 ASN cc_start: 0.9042 (m-40) cc_final: 0.8650 (m110) REVERT: A 460 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8116 (mmmt) REVERT: A 468 HIS cc_start: 0.7877 (t-90) cc_final: 0.7373 (t-90) REVERT: A 472 LEU cc_start: 0.8319 (mt) cc_final: 0.7901 (tp) REVERT: A 496 ILE cc_start: 0.7984 (mt) cc_final: 0.7450 (mt) REVERT: A 505 ILE cc_start: 0.8760 (mt) cc_final: 0.7978 (tt) REVERT: A 509 LEU cc_start: 0.8852 (tp) cc_final: 0.8513 (mt) REVERT: A 511 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7708 (mm-30) REVERT: A 512 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7957 (tt0) REVERT: A 520 ASP cc_start: 0.8392 (m-30) cc_final: 0.7567 (t0) REVERT: A 526 LYS cc_start: 0.9059 (tttt) cc_final: 0.8619 (mmtm) REVERT: A 528 TYR cc_start: 0.7906 (m-10) cc_final: 0.7536 (m-80) REVERT: A 534 LYS cc_start: 0.8488 (tptt) cc_final: 0.7993 (tptt) REVERT: A 535 CYS cc_start: 0.6907 (p) cc_final: 0.6435 (p) REVERT: A 543 MET cc_start: 0.5850 (mmt) cc_final: 0.5556 (mmt) REVERT: A 556 LYS cc_start: 0.8541 (mttt) cc_final: 0.8166 (mttm) REVERT: A 558 GLU cc_start: 0.7902 (tt0) cc_final: 0.7392 (tm-30) REVERT: A 559 TYR cc_start: 0.7650 (m-80) cc_final: 0.6653 (m-80) REVERT: A 575 GLU cc_start: 0.6891 (mp0) cc_final: 0.5517 (pt0) REVERT: A 587 MET cc_start: 0.7741 (mmt) cc_final: 0.7369 (tpp) REVERT: A 633 LYS cc_start: 0.6851 (mtmm) cc_final: 0.6610 (mtmm) REVERT: A 637 HIS cc_start: 0.8056 (t-90) cc_final: 0.7808 (t-90) REVERT: A 638 GLN cc_start: 0.9129 (tt0) cc_final: 0.8291 (mt0) REVERT: A 640 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.7991 (ptm160) REVERT: A 641 ASN cc_start: 0.8848 (m110) cc_final: 0.8509 (m110) REVERT: A 643 LEU cc_start: 0.8900 (tp) cc_final: 0.8054 (tp) REVERT: A 644 HIS cc_start: 0.7762 (m-70) cc_final: 0.7538 (m-70) REVERT: A 646 LEU cc_start: 0.8827 (tp) cc_final: 0.8309 (tt) REVERT: A 647 MET cc_start: 0.8154 (mmm) cc_final: 0.7312 (mmm) REVERT: A 650 LEU cc_start: 0.8238 (mm) cc_final: 0.8027 (mm) REVERT: A 657 TYR cc_start: 0.6858 (m-80) cc_final: 0.6385 (m-80) REVERT: A 750 PHE cc_start: 0.8241 (m-80) cc_final: 0.7894 (m-80) REVERT: A 757 TYR cc_start: 0.8667 (t80) cc_final: 0.8280 (t80) REVERT: B 17 LEU cc_start: 0.5987 (mt) cc_final: 0.5681 (mt) REVERT: B 34 SER cc_start: 0.7813 (p) cc_final: 0.7494 (p) REVERT: B 54 TYR cc_start: 0.7656 (m-80) cc_final: 0.6487 (m-80) REVERT: B 62 LYS cc_start: 0.8441 (mttm) cc_final: 0.7811 (mttm) REVERT: B 63 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6823 (ppt170) REVERT: B 73 GLU cc_start: 0.7820 (tt0) cc_final: 0.7318 (tm-30) REVERT: B 83 MET cc_start: 0.8324 (tpp) cc_final: 0.7669 (tpp) REVERT: B 84 GLU cc_start: 0.8680 (tt0) cc_final: 0.8327 (tm-30) REVERT: B 101 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8193 (tm-30) REVERT: B 102 HIS cc_start: 0.7942 (m90) cc_final: 0.6856 (m90) REVERT: B 117 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7653 (mtp180) REVERT: B 119 LYS cc_start: 0.8448 (tppt) cc_final: 0.7100 (mmmt) REVERT: B 121 THR cc_start: 0.8646 (p) cc_final: 0.8401 (p) REVERT: B 122 GLN cc_start: 0.8467 (tt0) cc_final: 0.7924 (tm-30) REVERT: B 123 ILE cc_start: 0.8730 (mt) cc_final: 0.7815 (mt) REVERT: B 124 MET cc_start: 0.8404 (tpp) cc_final: 0.7257 (tpp) REVERT: B 125 PHE cc_start: 0.7943 (m-10) cc_final: 0.7670 (m-10) REVERT: B 126 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 128 PHE cc_start: 0.7560 (m-80) cc_final: 0.6758 (m-10) REVERT: B 130 VAL cc_start: 0.8413 (t) cc_final: 0.7784 (p) REVERT: B 133 MET cc_start: 0.7391 (ttp) cc_final: 0.6767 (ttp) REVERT: B 163 ASN cc_start: 0.8333 (t0) cc_final: 0.7740 (t0) REVERT: B 168 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 179 LEU cc_start: 0.6623 (tp) cc_final: 0.6320 (tp) REVERT: B 194 LEU cc_start: 0.8676 (mt) cc_final: 0.8372 (mt) REVERT: B 206 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 212 ASP cc_start: 0.8911 (m-30) cc_final: 0.8066 (m-30) REVERT: B 214 LYS cc_start: 0.9159 (ttpt) cc_final: 0.8934 (ttpt) REVERT: B 216 LYS cc_start: 0.8746 (mttt) cc_final: 0.8467 (mmmm) REVERT: B 223 ASP cc_start: 0.7599 (t70) cc_final: 0.7248 (m-30) REVERT: B 256 PHE cc_start: 0.7957 (p90) cc_final: 0.7568 (p90) REVERT: B 257 ARG cc_start: 0.7454 (mtp180) cc_final: 0.7115 (ttp80) REVERT: B 263 PHE cc_start: 0.8379 (m-80) cc_final: 0.7272 (m-80) REVERT: B 272 SER cc_start: 0.8093 (m) cc_final: 0.7217 (p) REVERT: B 281 ASN cc_start: 0.8383 (m-40) cc_final: 0.7541 (m110) REVERT: B 291 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7652 (mtt180) REVERT: B 293 ASP cc_start: 0.8847 (m-30) cc_final: 0.8642 (m-30) REVERT: B 306 MET cc_start: 0.7111 (mmm) cc_final: 0.6707 (mmm) REVERT: B 313 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.7670 (tpp-160) REVERT: B 314 MET cc_start: 0.8587 (tpt) cc_final: 0.7767 (mmm) REVERT: B 315 GLN cc_start: 0.8221 (mt0) cc_final: 0.7702 (mm-40) REVERT: B 318 ILE cc_start: 0.8216 (mm) cc_final: 0.8008 (mt) REVERT: B 326 MET cc_start: 0.7222 (mmp) cc_final: 0.6894 (mmm) REVERT: B 330 ILE cc_start: 0.6067 (mm) cc_final: 0.5646 (mm) REVERT: B 335 GLU cc_start: 0.7804 (mp0) cc_final: 0.7448 (mp0) REVERT: B 358 ILE cc_start: 0.7504 (mp) cc_final: 0.7248 (mm) REVERT: B 372 HIS cc_start: 0.6878 (m-70) cc_final: 0.6592 (m-70) REVERT: C 53 TYR cc_start: 0.6965 (m-80) cc_final: 0.5961 (m-80) REVERT: C 57 GLU cc_start: 0.8013 (pt0) cc_final: 0.7328 (pt0) REVERT: C 64 ILE cc_start: 0.7911 (mt) cc_final: 0.7528 (mt) REVERT: C 82 MET cc_start: 0.7951 (tpp) cc_final: 0.6641 (tpp) REVERT: C 84 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8936 (ttmm) REVERT: C 87 HIS cc_start: 0.7794 (t70) cc_final: 0.7313 (t70) REVERT: C 90 PHE cc_start: 0.7694 (m-10) cc_final: 0.7356 (m-80) REVERT: C 91 TYR cc_start: 0.7630 (m-80) cc_final: 0.7401 (m-80) REVERT: C 99 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6294 (mp0) REVERT: C 100 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7880 (tp30) REVERT: C 115 ASN cc_start: 0.8080 (t0) cc_final: 0.7697 (t0) REVERT: C 118 LYS cc_start: 0.8297 (tptt) cc_final: 0.7441 (tptt) REVERT: C 123 MET cc_start: 0.8283 (tpp) cc_final: 0.7124 (tpp) REVERT: C 127 PHE cc_start: 0.8273 (m-80) cc_final: 0.7687 (m-80) REVERT: C 136 ILE cc_start: 0.8385 (mm) cc_final: 0.7920 (tp) REVERT: C 139 VAL cc_start: 0.8838 (m) cc_final: 0.8273 (m) REVERT: C 152 VAL cc_start: 0.8126 (p) cc_final: 0.7902 (m) REVERT: C 157 ASP cc_start: 0.6574 (t0) cc_final: 0.6215 (t0) REVERT: C 161 HIS cc_start: 0.6639 (p90) cc_final: 0.6199 (p90) REVERT: C 167 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 169 TYR cc_start: 0.7234 (m-80) cc_final: 0.7017 (t80) REVERT: C 176 MET cc_start: 0.6122 (mtt) cc_final: 0.5080 (mtt) REVERT: C 186 THR cc_start: 0.8936 (m) cc_final: 0.8417 (p) REVERT: C 187 ASP cc_start: 0.8988 (m-30) cc_final: 0.8646 (m-30) REVERT: C 190 MET cc_start: 0.8659 (mtm) cc_final: 0.8120 (mtm) REVERT: C 198 TYR cc_start: 0.5412 (m-10) cc_final: 0.5057 (m-80) REVERT: C 205 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 207 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7397 (tp30) REVERT: C 218 TYR cc_start: 0.5565 (p90) cc_final: 0.4488 (p90) REVERT: C 256 ARG cc_start: 0.7738 (mtp180) cc_final: 0.6765 (mtp180) REVERT: C 280 ASN cc_start: 0.8829 (m-40) cc_final: 0.8037 (m-40) REVERT: C 282 ILE cc_start: 0.8599 (mt) cc_final: 0.8391 (mt) REVERT: C 283 MET cc_start: 0.8309 (mmm) cc_final: 0.7959 (mmm) REVERT: C 284 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8069 (mtpt) REVERT: C 286 ASP cc_start: 0.8287 (t0) cc_final: 0.7956 (p0) REVERT: C 287 ILE cc_start: 0.8242 (tt) cc_final: 0.7894 (tp) REVERT: C 289 ILE cc_start: 0.8014 (pt) cc_final: 0.7811 (mm) REVERT: C 290 ARG cc_start: 0.7162 (mtt180) cc_final: 0.5963 (mtt90) REVERT: C 294 TYR cc_start: 0.7987 (m-80) cc_final: 0.7325 (m-80) REVERT: C 299 MET cc_start: 0.7984 (mmm) cc_final: 0.7180 (mmm) REVERT: C 303 THR cc_start: 0.8715 (m) cc_final: 0.8433 (p) REVERT: C 305 MET cc_start: 0.6117 (mmm) cc_final: 0.5630 (mmp) REVERT: C 306 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6995 (t80) REVERT: C 313 MET cc_start: 0.8469 (tpp) cc_final: 0.6905 (tpp) REVERT: C 314 GLN cc_start: 0.8570 (tt0) cc_final: 0.8010 (tt0) REVERT: C 315 LYS cc_start: 0.8781 (tttp) cc_final: 0.8434 (tttp) REVERT: C 317 ILE cc_start: 0.8942 (mm) cc_final: 0.8068 (mm) REVERT: C 328 LYS cc_start: 0.8133 (mttm) cc_final: 0.7897 (mttm) REVERT: D 8 LEU cc_start: 0.7749 (mt) cc_final: 0.7510 (mt) REVERT: D 9 VAL cc_start: 0.7495 (m) cc_final: 0.7138 (p) REVERT: D 11 ASP cc_start: 0.7274 (t70) cc_final: 0.6975 (t0) REVERT: D 16 LEU cc_start: 0.8653 (tp) cc_final: 0.8443 (tp) REVERT: D 34 ILE cc_start: 0.8062 (mt) cc_final: 0.7499 (tp) REVERT: D 51 ASP cc_start: 0.6178 (p0) cc_final: 0.5187 (p0) REVERT: D 52 SER cc_start: 0.6757 (t) cc_final: 0.6391 (m) REVERT: D 57 GLU cc_start: 0.8200 (tt0) cc_final: 0.7194 (tt0) REVERT: D 61 LYS cc_start: 0.8142 (mttm) cc_final: 0.7689 (mttt) REVERT: D 62 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6663 (mtt90) REVERT: D 66 THR cc_start: 0.7084 (t) cc_final: 0.6020 (p) REVERT: D 68 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7053 (mmtt) REVERT: D 87 HIS cc_start: 0.8541 (t-90) cc_final: 0.8334 (t-90) REVERT: D 101 HIS cc_start: 0.6985 (m-70) cc_final: 0.6735 (m90) REVERT: D 115 ASN cc_start: 0.8594 (t0) cc_final: 0.8375 (t0) REVERT: D 118 LYS cc_start: 0.8934 (tptt) cc_final: 0.8238 (tppt) REVERT: D 119 MET cc_start: 0.8412 (ttm) cc_final: 0.8048 (ttm) REVERT: D 137 GLN cc_start: 0.7902 (mt0) cc_final: 0.7562 (mt0) REVERT: D 139 VAL cc_start: 0.8693 (m) cc_final: 0.7587 (p) REVERT: D 143 TYR cc_start: 0.6909 (m-10) cc_final: 0.6316 (m-80) REVERT: D 166 TYR cc_start: 0.7802 (t80) cc_final: 0.7582 (t80) REVERT: D 167 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 175 ILE cc_start: 0.7477 (pt) cc_final: 0.6085 (mm) REVERT: D 176 MET cc_start: 0.6798 (mmm) cc_final: 0.6534 (mmm) REVERT: D 186 THR cc_start: 0.8914 (m) cc_final: 0.8600 (p) REVERT: D 187 ASP cc_start: 0.8526 (m-30) cc_final: 0.8282 (m-30) REVERT: D 190 MET cc_start: 0.8305 (mtm) cc_final: 0.8084 (mtm) REVERT: D 205 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 206 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7783 (ttm-80) REVERT: D 207 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7452 (tp30) REVERT: D 209 VAL cc_start: 0.8690 (t) cc_final: 0.8440 (t) REVERT: D 212 ILE cc_start: 0.8823 (mt) cc_final: 0.8374 (mt) REVERT: D 215 LYS cc_start: 0.8608 (mttt) cc_final: 0.8350 (ptpp) REVERT: D 216 LEU cc_start: 0.7508 (mt) cc_final: 0.7252 (mt) REVERT: D 252 ASN cc_start: 0.8080 (t0) cc_final: 0.7142 (t0) REVERT: D 284 LYS cc_start: 0.8635 (mttm) cc_final: 0.8329 (tptp) REVERT: D 288 ASP cc_start: 0.8585 (m-30) cc_final: 0.8356 (p0) REVERT: D 290 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6216 (mtm-85) REVERT: D 294 TYR cc_start: 0.8096 (m-80) cc_final: 0.7554 (m-80) REVERT: D 299 MET cc_start: 0.8154 (mmm) cc_final: 0.7435 (mmm) REVERT: D 303 THR cc_start: 0.7377 (m) cc_final: 0.7031 (p) REVERT: D 314 GLN cc_start: 0.8844 (tt0) cc_final: 0.8630 (tm-30) REVERT: D 329 ILE cc_start: 0.8002 (mm) cc_final: 0.7001 (mm) outliers start: 4 outliers final: 2 residues processed: 816 average time/residue: 0.3199 time to fit residues: 360.2530 Evaluate side-chains 730 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 727 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 168 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 430 HIS A 525 GLN A 552 HIS A 576 GLN A 742 GLN B 79 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 173 HIS C 263 GLN C 280 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093465 restraints weight = 41593.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097425 restraints weight = 25916.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100219 restraints weight = 17937.962| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15177 Z= 0.220 Angle : 0.685 8.854 20547 Z= 0.351 Chirality : 0.044 0.208 2251 Planarity : 0.005 0.060 2631 Dihedral : 10.085 166.840 2071 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1847 helix: 0.57 (0.18), residues: 832 sheet: -1.49 (0.28), residues: 288 loop : -0.11 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 357 HIS 0.009 0.001 HIS D 371 PHE 0.023 0.002 PHE D 124 TYR 0.028 0.002 TYR A 439 ARG 0.014 0.001 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 766 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7409 (mm-30) REVERT: A 87 HIS cc_start: 0.8472 (t-90) cc_final: 0.8160 (t-90) REVERT: A 89 LEU cc_start: 0.8459 (mt) cc_final: 0.8111 (pp) REVERT: A 94 ILE cc_start: 0.8391 (mt) cc_final: 0.7775 (tp) REVERT: A 99 ILE cc_start: 0.8181 (pt) cc_final: 0.7860 (pt) REVERT: A 110 ILE cc_start: 0.7885 (mp) cc_final: 0.7373 (tp) REVERT: A 121 GLU cc_start: 0.8521 (tp30) cc_final: 0.8147 (tp30) REVERT: A 122 ASP cc_start: 0.9217 (m-30) cc_final: 0.8948 (p0) REVERT: A 125 ASN cc_start: 0.9288 (m-40) cc_final: 0.8930 (m110) REVERT: A 144 GLU cc_start: 0.8606 (tp30) cc_final: 0.8362 (tm-30) REVERT: A 150 MET cc_start: 0.7891 (ttp) cc_final: 0.7645 (ttp) REVERT: A 179 TYR cc_start: 0.8681 (t80) cc_final: 0.8179 (t80) REVERT: A 200 ASN cc_start: 0.9181 (m-40) cc_final: 0.8855 (m110) REVERT: A 225 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7084 (mp0) REVERT: A 239 MET cc_start: 0.7152 (mmp) cc_final: 0.6774 (mmp) REVERT: A 242 TYR cc_start: 0.7209 (m-80) cc_final: 0.6816 (m-80) REVERT: A 248 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7569 (tpp80) REVERT: A 256 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7145 (mp0) REVERT: A 259 TYR cc_start: 0.7742 (m-80) cc_final: 0.6815 (m-80) REVERT: A 262 PHE cc_start: 0.8825 (m-80) cc_final: 0.7723 (m-80) REVERT: A 286 HIS cc_start: 0.6288 (t-90) cc_final: 0.6086 (t-90) REVERT: A 307 HIS cc_start: 0.8916 (m90) cc_final: 0.8501 (m90) REVERT: A 312 CYS cc_start: 0.8505 (m) cc_final: 0.8128 (m) REVERT: A 315 LEU cc_start: 0.7051 (mt) cc_final: 0.6808 (mt) REVERT: A 317 ILE cc_start: 0.8475 (mt) cc_final: 0.8127 (mt) REVERT: A 322 GLN cc_start: 0.8752 (mt0) cc_final: 0.8533 (mt0) REVERT: A 325 ILE cc_start: 0.9101 (tt) cc_final: 0.8844 (pt) REVERT: A 354 HIS cc_start: 0.6823 (t-170) cc_final: 0.6291 (t-170) REVERT: A 358 THR cc_start: 0.8381 (m) cc_final: 0.7922 (m) REVERT: A 364 MET cc_start: 0.7489 (mtt) cc_final: 0.7184 (mtt) REVERT: A 370 GLU cc_start: 0.8385 (tt0) cc_final: 0.8036 (tt0) REVERT: A 371 MET cc_start: 0.9068 (mtm) cc_final: 0.8507 (mpp) REVERT: A 373 HIS cc_start: 0.8480 (t70) cc_final: 0.8082 (t70) REVERT: A 408 TYR cc_start: 0.8801 (t80) cc_final: 0.7972 (t80) REVERT: A 417 ASP cc_start: 0.8732 (m-30) cc_final: 0.8453 (t0) REVERT: A 423 LEU cc_start: 0.6785 (mt) cc_final: 0.6569 (mt) REVERT: A 432 PHE cc_start: 0.7065 (p90) cc_final: 0.6784 (p90) REVERT: A 448 SER cc_start: 0.8153 (m) cc_final: 0.7902 (p) REVERT: A 451 GLN cc_start: 0.8751 (mp10) cc_final: 0.8439 (mp10) REVERT: A 453 CYS cc_start: 0.8708 (m) cc_final: 0.8503 (p) REVERT: A 458 ASN cc_start: 0.9141 (m-40) cc_final: 0.8809 (m110) REVERT: A 460 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8759 (tppt) REVERT: A 467 MET cc_start: 0.8540 (mtm) cc_final: 0.8109 (mtm) REVERT: A 468 HIS cc_start: 0.8163 (t-90) cc_final: 0.7740 (t-90) REVERT: A 475 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8191 (pp20) REVERT: A 476 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8230 (tm-30) REVERT: A 478 MET cc_start: 0.8877 (mtm) cc_final: 0.8542 (mtm) REVERT: A 498 LEU cc_start: 0.8962 (mp) cc_final: 0.8377 (tt) REVERT: A 509 LEU cc_start: 0.8999 (tp) cc_final: 0.8669 (mt) REVERT: A 512 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7807 (mt-10) REVERT: A 514 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8331 (ptmm) REVERT: A 520 ASP cc_start: 0.8403 (m-30) cc_final: 0.8143 (p0) REVERT: A 521 ASP cc_start: 0.8698 (p0) cc_final: 0.8388 (p0) REVERT: A 525 GLN cc_start: 0.8341 (tp40) cc_final: 0.7484 (tp-100) REVERT: A 526 LYS cc_start: 0.8999 (tttt) cc_final: 0.8435 (mmmt) REVERT: A 528 TYR cc_start: 0.7894 (m-10) cc_final: 0.7673 (m-10) REVERT: A 535 CYS cc_start: 0.6022 (p) cc_final: 0.5717 (p) REVERT: A 555 ASP cc_start: 0.8147 (t0) cc_final: 0.7913 (t0) REVERT: A 556 LYS cc_start: 0.8719 (mttt) cc_final: 0.8023 (mtpp) REVERT: A 558 GLU cc_start: 0.7875 (tt0) cc_final: 0.7427 (tm-30) REVERT: A 559 TYR cc_start: 0.7558 (m-80) cc_final: 0.7086 (m-80) REVERT: A 560 GLN cc_start: 0.7207 (mp10) cc_final: 0.6442 (mp10) REVERT: A 568 ASN cc_start: 0.8081 (t0) cc_final: 0.7840 (t0) REVERT: A 579 VAL cc_start: 0.9121 (m) cc_final: 0.8876 (t) REVERT: A 637 HIS cc_start: 0.8315 (t-90) cc_final: 0.8020 (t-90) REVERT: A 638 GLN cc_start: 0.9011 (tt0) cc_final: 0.8709 (pt0) REVERT: A 640 ARG cc_start: 0.8645 (ptp-170) cc_final: 0.8264 (ptp-170) REVERT: A 641 ASN cc_start: 0.9039 (m110) cc_final: 0.8580 (m-40) REVERT: A 643 LEU cc_start: 0.8782 (tp) cc_final: 0.7959 (tp) REVERT: A 646 LEU cc_start: 0.8974 (tp) cc_final: 0.8767 (pp) REVERT: A 657 TYR cc_start: 0.6721 (m-80) cc_final: 0.6231 (m-80) REVERT: A 757 TYR cc_start: 0.8845 (t80) cc_final: 0.8481 (t80) REVERT: B 54 TYR cc_start: 0.7597 (m-80) cc_final: 0.6912 (m-10) REVERT: B 62 LYS cc_start: 0.8469 (mttm) cc_final: 0.7676 (mttm) REVERT: B 66 LEU cc_start: 0.8302 (mt) cc_final: 0.8021 (mt) REVERT: B 77 ILE cc_start: 0.8704 (mm) cc_final: 0.8182 (tt) REVERT: B 83 MET cc_start: 0.8238 (tpp) cc_final: 0.7575 (tpp) REVERT: B 84 GLU cc_start: 0.8754 (tt0) cc_final: 0.8390 (tm-30) REVERT: B 85 LYS cc_start: 0.9106 (mttm) cc_final: 0.8877 (mttm) REVERT: B 106 LEU cc_start: 0.7779 (mt) cc_final: 0.7247 (mt) REVERT: B 119 LYS cc_start: 0.8493 (tppt) cc_final: 0.6807 (tppt) REVERT: B 120 MET cc_start: 0.8560 (ttm) cc_final: 0.7719 (tmm) REVERT: B 122 GLN cc_start: 0.8461 (tt0) cc_final: 0.8146 (tm-30) REVERT: B 123 ILE cc_start: 0.8582 (mt) cc_final: 0.7744 (mt) REVERT: B 124 MET cc_start: 0.8384 (tpp) cc_final: 0.7546 (tpp) REVERT: B 126 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 128 PHE cc_start: 0.8032 (m-80) cc_final: 0.6857 (m-10) REVERT: B 129 ASN cc_start: 0.8493 (m-40) cc_final: 0.8283 (m-40) REVERT: B 133 MET cc_start: 0.7578 (ttp) cc_final: 0.6332 (ttp) REVERT: B 134 TYR cc_start: 0.7296 (t80) cc_final: 0.7052 (t80) REVERT: B 163 ASN cc_start: 0.8287 (t0) cc_final: 0.7790 (t0) REVERT: B 168 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 174 HIS cc_start: 0.7680 (p-80) cc_final: 0.7157 (p-80) REVERT: B 177 MET cc_start: 0.7123 (mmm) cc_final: 0.6727 (mmm) REVERT: B 181 LEU cc_start: 0.7845 (tp) cc_final: 0.7601 (tp) REVERT: B 186 LEU cc_start: 0.8145 (mt) cc_final: 0.7810 (mt) REVERT: B 194 LEU cc_start: 0.8843 (mt) cc_final: 0.8607 (mt) REVERT: B 207 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8217 (ttm170) REVERT: B 208 GLU cc_start: 0.7706 (pp20) cc_final: 0.7407 (tm-30) REVERT: B 212 ASP cc_start: 0.9024 (m-30) cc_final: 0.7934 (m-30) REVERT: B 214 LYS cc_start: 0.9055 (ttpt) cc_final: 0.8511 (ttpt) REVERT: B 239 LYS cc_start: 0.8603 (mttt) cc_final: 0.8375 (mmtt) REVERT: B 256 PHE cc_start: 0.8165 (p90) cc_final: 0.7920 (p90) REVERT: B 260 GLU cc_start: 0.8399 (tp30) cc_final: 0.7947 (tm-30) REVERT: B 263 PHE cc_start: 0.8451 (m-80) cc_final: 0.7427 (m-80) REVERT: B 264 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7450 (mt0) REVERT: B 277 GLU cc_start: 0.7920 (tp30) cc_final: 0.7227 (tp30) REVERT: B 281 ASN cc_start: 0.8026 (m-40) cc_final: 0.7756 (m-40) REVERT: B 285 LYS cc_start: 0.8407 (mmmm) cc_final: 0.7945 (mtmm) REVERT: B 291 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7527 (mtt180) REVERT: B 306 MET cc_start: 0.6994 (mmm) cc_final: 0.5689 (mmt) REVERT: B 313 ARG cc_start: 0.8734 (tpt-90) cc_final: 0.7862 (tpp-160) REVERT: B 314 MET cc_start: 0.8453 (tpt) cc_final: 0.7780 (mmp) REVERT: B 316 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8505 (ptpt) REVERT: B 326 MET cc_start: 0.7421 (mmp) cc_final: 0.6892 (mmm) REVERT: B 335 GLU cc_start: 0.8232 (mp0) cc_final: 0.7665 (mp0) REVERT: B 353 PHE cc_start: 0.8037 (t80) cc_final: 0.7377 (t80) REVERT: B 356 MET cc_start: 0.8560 (mtt) cc_final: 0.8212 (mmm) REVERT: B 361 GLN cc_start: 0.8947 (pp30) cc_final: 0.8718 (pp30) REVERT: B 372 HIS cc_start: 0.7118 (m-70) cc_final: 0.6759 (m-70) REVERT: C 51 ASP cc_start: 0.7858 (p0) cc_final: 0.7075 (p0) REVERT: C 54 VAL cc_start: 0.7598 (t) cc_final: 0.6982 (p) REVERT: C 64 ILE cc_start: 0.7865 (mt) cc_final: 0.7283 (tp) REVERT: C 71 ILE cc_start: 0.7391 (mm) cc_final: 0.7031 (tp) REVERT: C 72 GLU cc_start: 0.8343 (pp20) cc_final: 0.8058 (pp20) REVERT: C 79 TRP cc_start: 0.6907 (m100) cc_final: 0.6523 (m100) REVERT: C 82 MET cc_start: 0.8054 (tpp) cc_final: 0.6900 (tpp) REVERT: C 87 HIS cc_start: 0.8174 (t70) cc_final: 0.7610 (t-90) REVERT: C 90 PHE cc_start: 0.7594 (m-10) cc_final: 0.7169 (m-80) REVERT: C 91 TYR cc_start: 0.7832 (m-80) cc_final: 0.7367 (m-80) REVERT: C 111 ASN cc_start: 0.8512 (t0) cc_final: 0.7829 (t0) REVERT: C 118 LYS cc_start: 0.8170 (tptt) cc_final: 0.7498 (tptt) REVERT: C 119 MET cc_start: 0.8434 (ttm) cc_final: 0.8208 (ttm) REVERT: C 121 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8582 (tm-30) REVERT: C 123 MET cc_start: 0.8136 (tpp) cc_final: 0.7048 (tpp) REVERT: C 124 PHE cc_start: 0.7717 (m-80) cc_final: 0.7328 (m-80) REVERT: C 127 PHE cc_start: 0.8013 (m-80) cc_final: 0.7650 (m-80) REVERT: C 136 ILE cc_start: 0.8492 (mm) cc_final: 0.7870 (tp) REVERT: C 140 LEU cc_start: 0.8461 (mt) cc_final: 0.8186 (mt) REVERT: C 157 ASP cc_start: 0.6880 (t0) cc_final: 0.6469 (t0) REVERT: C 161 HIS cc_start: 0.6933 (p-80) cc_final: 0.6630 (p-80) REVERT: C 167 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8065 (mm-30) REVERT: C 169 TYR cc_start: 0.7697 (m-80) cc_final: 0.7367 (t80) REVERT: C 176 MET cc_start: 0.6330 (mtt) cc_final: 0.5731 (mtt) REVERT: C 191 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8705 (mtpp) REVERT: C 192 ILE cc_start: 0.8523 (pt) cc_final: 0.8119 (mm) REVERT: C 202 THR cc_start: 0.7628 (p) cc_final: 0.6957 (p) REVERT: C 205 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 207 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7929 (tm-30) REVERT: C 211 ASP cc_start: 0.8476 (m-30) cc_final: 0.7428 (m-30) REVERT: C 212 ILE cc_start: 0.8879 (mt) cc_final: 0.8679 (mt) REVERT: C 242 LEU cc_start: 0.8553 (mt) cc_final: 0.7792 (mt) REVERT: C 256 ARG cc_start: 0.8468 (mtp180) cc_final: 0.7484 (mtp180) REVERT: C 259 GLU cc_start: 0.8821 (tp30) cc_final: 0.7650 (tm-30) REVERT: C 260 THR cc_start: 0.8428 (m) cc_final: 0.8220 (p) REVERT: C 262 PHE cc_start: 0.8701 (m-10) cc_final: 0.8413 (m-10) REVERT: C 263 GLN cc_start: 0.7918 (mt0) cc_final: 0.7186 (mt0) REVERT: C 276 GLU cc_start: 0.8510 (tp30) cc_final: 0.7848 (tp30) REVERT: C 280 ASN cc_start: 0.8590 (m110) cc_final: 0.7957 (m110) REVERT: C 282 ILE cc_start: 0.8566 (mt) cc_final: 0.8311 (mt) REVERT: C 283 MET cc_start: 0.8287 (mmm) cc_final: 0.7854 (mmm) REVERT: C 284 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8204 (mtpp) REVERT: C 286 ASP cc_start: 0.8271 (t0) cc_final: 0.7439 (p0) REVERT: C 294 TYR cc_start: 0.7763 (m-80) cc_final: 0.7456 (m-80) REVERT: C 296 ASN cc_start: 0.7570 (p0) cc_final: 0.7140 (p0) REVERT: C 299 MET cc_start: 0.8141 (mmm) cc_final: 0.7668 (mmm) REVERT: C 303 THR cc_start: 0.8438 (m) cc_final: 0.8217 (p) REVERT: C 313 MET cc_start: 0.8478 (tpp) cc_final: 0.7511 (tpp) REVERT: C 314 GLN cc_start: 0.8577 (tt0) cc_final: 0.7990 (tt0) REVERT: C 316 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 327 ILE cc_start: 0.8664 (mm) cc_final: 0.8160 (pt) REVERT: C 329 ILE cc_start: 0.8340 (mm) cc_final: 0.7995 (mt) REVERT: C 356 TRP cc_start: 0.7208 (m100) cc_final: 0.6762 (m100) REVERT: C 361 GLU cc_start: 0.8573 (tp30) cc_final: 0.8023 (tp30) REVERT: D 12 ASN cc_start: 0.7414 (m110) cc_final: 0.6948 (m110) REVERT: D 34 ILE cc_start: 0.8333 (mt) cc_final: 0.7874 (mp) REVERT: D 44 MET cc_start: 0.6171 (mmm) cc_final: 0.5770 (mmm) REVERT: D 49 GLN cc_start: 0.6755 (pm20) cc_final: 0.6514 (pm20) REVERT: D 50 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7330 (mtmm) REVERT: D 51 ASP cc_start: 0.6661 (p0) cc_final: 0.5723 (p0) REVERT: D 52 SER cc_start: 0.7283 (t) cc_final: 0.6956 (m) REVERT: D 57 GLU cc_start: 0.8323 (tt0) cc_final: 0.7420 (tt0) REVERT: D 61 LYS cc_start: 0.8208 (mttm) cc_final: 0.7751 (mttt) REVERT: D 62 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7244 (mtt90) REVERT: D 68 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7307 (mmtt) REVERT: D 86 TRP cc_start: 0.8069 (m-10) cc_final: 0.7130 (m-90) REVERT: D 94 LEU cc_start: 0.8244 (mt) cc_final: 0.7880 (mt) REVERT: D 107 GLU cc_start: 0.7106 (pt0) cc_final: 0.5701 (pt0) REVERT: D 111 ASN cc_start: 0.7910 (m-40) cc_final: 0.6636 (m-40) REVERT: D 116 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: D 117 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8158 (mt-10) REVERT: D 118 LYS cc_start: 0.9135 (tptt) cc_final: 0.7635 (tppt) REVERT: D 119 MET cc_start: 0.9029 (ttm) cc_final: 0.8292 (ttm) REVERT: D 123 MET cc_start: 0.8135 (mmp) cc_final: 0.7756 (mmp) REVERT: D 125 GLU cc_start: 0.8815 (pt0) cc_final: 0.8447 (pt0) REVERT: D 133 TYR cc_start: 0.7391 (t80) cc_final: 0.7117 (t80) REVERT: D 137 GLN cc_start: 0.8085 (mt0) cc_final: 0.7672 (mt0) REVERT: D 139 VAL cc_start: 0.8644 (m) cc_final: 0.8287 (p) REVERT: D 165 ILE cc_start: 0.7758 (mt) cc_final: 0.7447 (tt) REVERT: D 176 MET cc_start: 0.6949 (mmm) cc_final: 0.6671 (mmm) REVERT: D 187 ASP cc_start: 0.8702 (m-30) cc_final: 0.8421 (m-30) REVERT: D 191 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8818 (ttpt) REVERT: D 205 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 207 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7451 (tp30) REVERT: D 209 VAL cc_start: 0.8724 (t) cc_final: 0.8407 (t) REVERT: D 211 ASP cc_start: 0.8834 (m-30) cc_final: 0.7509 (m-30) REVERT: D 213 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8293 (ttpt) REVERT: D 214 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7494 (mm-30) REVERT: D 238 LYS cc_start: 0.7049 (mttm) cc_final: 0.6823 (mmtm) REVERT: D 240 TYR cc_start: 0.7873 (t80) cc_final: 0.7510 (t80) REVERT: D 263 GLN cc_start: 0.8067 (mt0) cc_final: 0.7782 (tm-30) REVERT: D 286 ASP cc_start: 0.8294 (t0) cc_final: 0.7898 (t0) REVERT: D 288 ASP cc_start: 0.8700 (m-30) cc_final: 0.8107 (m-30) REVERT: D 290 ARG cc_start: 0.7579 (mtt180) cc_final: 0.6616 (mtt180) REVERT: D 294 TYR cc_start: 0.8261 (m-80) cc_final: 0.7660 (m-80) REVERT: D 299 MET cc_start: 0.8079 (mmm) cc_final: 0.7505 (mmm) REVERT: D 303 THR cc_start: 0.7776 (m) cc_final: 0.7387 (p) REVERT: D 309 ILE cc_start: 0.8346 (tt) cc_final: 0.8102 (tp) REVERT: D 312 ARG cc_start: 0.8889 (tpt-90) cc_final: 0.7535 (tpp80) REVERT: D 314 GLN cc_start: 0.8962 (tt0) cc_final: 0.8681 (tm-30) REVERT: D 316 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7814 (mm-30) outliers start: 1 outliers final: 0 residues processed: 766 average time/residue: 0.3239 time to fit residues: 342.0530 Evaluate side-chains 691 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 691 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 286 HIS A 334 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 HIS A 680 GLN B 162 HIS B 315 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 12 ASN D 40 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086743 restraints weight = 42750.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090487 restraints weight = 25874.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093167 restraints weight = 17576.156| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15177 Z= 0.294 Angle : 0.720 7.658 20547 Z= 0.377 Chirality : 0.045 0.186 2251 Planarity : 0.006 0.064 2631 Dihedral : 9.727 165.642 2071 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1847 helix: 0.75 (0.18), residues: 835 sheet: -1.48 (0.28), residues: 301 loop : -0.10 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.013 0.002 HIS A 644 PHE 0.017 0.002 PHE A 672 TYR 0.024 0.002 TYR A 477 ARG 0.008 0.001 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 767 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7385 (mm-30) REVERT: A 89 LEU cc_start: 0.8410 (mt) cc_final: 0.8061 (pp) REVERT: A 99 ILE cc_start: 0.8104 (pt) cc_final: 0.7767 (pt) REVERT: A 110 ILE cc_start: 0.7588 (mp) cc_final: 0.7122 (tp) REVERT: A 116 LEU cc_start: 0.8836 (tp) cc_final: 0.8628 (tp) REVERT: A 122 ASP cc_start: 0.9181 (m-30) cc_final: 0.8646 (p0) REVERT: A 130 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8537 (mm110) REVERT: A 144 GLU cc_start: 0.8724 (tp30) cc_final: 0.8387 (tm-30) REVERT: A 150 MET cc_start: 0.8346 (ttp) cc_final: 0.7964 (ttp) REVERT: A 179 TYR cc_start: 0.8526 (t80) cc_final: 0.8096 (t80) REVERT: A 194 GLU cc_start: 0.7185 (tp30) cc_final: 0.6820 (tm-30) REVERT: A 223 TYR cc_start: 0.7660 (t80) cc_final: 0.7064 (t80) REVERT: A 224 ILE cc_start: 0.8613 (pt) cc_final: 0.8054 (pt) REVERT: A 248 ARG cc_start: 0.8500 (tpp80) cc_final: 0.7522 (tpp-160) REVERT: A 259 TYR cc_start: 0.7688 (m-80) cc_final: 0.6586 (m-80) REVERT: A 260 HIS cc_start: 0.8366 (m-70) cc_final: 0.8129 (m90) REVERT: A 262 PHE cc_start: 0.8771 (m-80) cc_final: 0.8061 (m-80) REVERT: A 286 HIS cc_start: 0.6727 (t70) cc_final: 0.6406 (t-90) REVERT: A 307 HIS cc_start: 0.8853 (m90) cc_final: 0.8628 (m90) REVERT: A 312 CYS cc_start: 0.8548 (m) cc_final: 0.8177 (m) REVERT: A 315 LEU cc_start: 0.7247 (mt) cc_final: 0.6938 (mt) REVERT: A 317 ILE cc_start: 0.8581 (mt) cc_final: 0.8199 (mt) REVERT: A 327 ARG cc_start: 0.8580 (mpt180) cc_final: 0.8263 (mmt-90) REVERT: A 370 GLU cc_start: 0.8419 (tt0) cc_final: 0.8108 (tt0) REVERT: A 371 MET cc_start: 0.9033 (mtm) cc_final: 0.8533 (mtp) REVERT: A 373 HIS cc_start: 0.8488 (t70) cc_final: 0.8055 (t70) REVERT: A 408 TYR cc_start: 0.8780 (t80) cc_final: 0.7924 (t80) REVERT: A 417 ASP cc_start: 0.8596 (m-30) cc_final: 0.8387 (m-30) REVERT: A 423 LEU cc_start: 0.7363 (mt) cc_final: 0.6950 (mt) REVERT: A 450 GLU cc_start: 0.8834 (mp0) cc_final: 0.8453 (pm20) REVERT: A 452 PHE cc_start: 0.8564 (t80) cc_final: 0.8136 (t80) REVERT: A 453 CYS cc_start: 0.8798 (m) cc_final: 0.8568 (p) REVERT: A 463 GLN cc_start: 0.8991 (tt0) cc_final: 0.8337 (mm110) REVERT: A 468 HIS cc_start: 0.8188 (t-90) cc_final: 0.7788 (t-90) REVERT: A 472 LEU cc_start: 0.8447 (mt) cc_final: 0.8081 (mt) REVERT: A 478 MET cc_start: 0.8841 (mtm) cc_final: 0.8481 (mtm) REVERT: A 493 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8178 (tp-100) REVERT: A 498 LEU cc_start: 0.9040 (mp) cc_final: 0.8432 (tt) REVERT: A 512 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 525 GLN cc_start: 0.8437 (tp40) cc_final: 0.7570 (tp-100) REVERT: A 526 LYS cc_start: 0.9024 (tttt) cc_final: 0.8361 (mmmt) REVERT: A 529 ASN cc_start: 0.8609 (m-40) cc_final: 0.7626 (m-40) REVERT: A 532 LEU cc_start: 0.7875 (mt) cc_final: 0.7257 (mt) REVERT: A 537 LEU cc_start: 0.8951 (mp) cc_final: 0.8665 (mp) REVERT: A 538 PHE cc_start: 0.8200 (t80) cc_final: 0.7868 (t80) REVERT: A 556 LYS cc_start: 0.8650 (mttt) cc_final: 0.8195 (mttm) REVERT: A 558 GLU cc_start: 0.7905 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 559 TYR cc_start: 0.7540 (m-80) cc_final: 0.7068 (m-80) REVERT: A 568 ASN cc_start: 0.8233 (t0) cc_final: 0.7888 (t0) REVERT: A 586 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7822 (mtmm) REVERT: A 637 HIS cc_start: 0.8377 (t-90) cc_final: 0.7880 (t-90) REVERT: A 638 GLN cc_start: 0.9022 (tt0) cc_final: 0.8708 (pt0) REVERT: A 640 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8288 (ptm-80) REVERT: A 641 ASN cc_start: 0.9023 (m110) cc_final: 0.8632 (m110) REVERT: A 643 LEU cc_start: 0.8842 (tp) cc_final: 0.8420 (tp) REVERT: A 648 GLU cc_start: 0.8900 (tp30) cc_final: 0.8517 (tm-30) REVERT: A 657 TYR cc_start: 0.6665 (m-80) cc_final: 0.6047 (m-80) REVERT: A 666 PHE cc_start: 0.8442 (m-10) cc_final: 0.8122 (m-10) REVERT: A 676 ARG cc_start: 0.8523 (mmp80) cc_final: 0.7429 (ttm110) REVERT: A 688 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 757 TYR cc_start: 0.8894 (t80) cc_final: 0.8525 (t80) REVERT: B 17 LEU cc_start: 0.7066 (mt) cc_final: 0.6849 (mt) REVERT: B 54 TYR cc_start: 0.7934 (m-80) cc_final: 0.7142 (m-10) REVERT: B 66 LEU cc_start: 0.8382 (mt) cc_final: 0.8070 (mt) REVERT: B 76 ILE cc_start: 0.8545 (pt) cc_final: 0.8262 (pt) REVERT: B 83 MET cc_start: 0.8315 (tpp) cc_final: 0.7713 (tpp) REVERT: B 84 GLU cc_start: 0.8788 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 85 LYS cc_start: 0.9199 (mttm) cc_final: 0.8895 (mttm) REVERT: B 106 LEU cc_start: 0.7974 (mt) cc_final: 0.7509 (mt) REVERT: B 114 LYS cc_start: 0.8537 (ptmm) cc_final: 0.7672 (ptmm) REVERT: B 120 MET cc_start: 0.8533 (ttm) cc_final: 0.7900 (tmm) REVERT: B 121 THR cc_start: 0.8639 (p) cc_final: 0.7864 (p) REVERT: B 123 ILE cc_start: 0.8641 (mt) cc_final: 0.7931 (mt) REVERT: B 124 MET cc_start: 0.8385 (tpp) cc_final: 0.7773 (tpp) REVERT: B 126 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 128 PHE cc_start: 0.8197 (m-80) cc_final: 0.7265 (m-10) REVERT: B 133 MET cc_start: 0.7358 (ttp) cc_final: 0.6597 (ttp) REVERT: B 134 TYR cc_start: 0.7370 (t80) cc_final: 0.7029 (t80) REVERT: B 166 ILE cc_start: 0.7713 (mm) cc_final: 0.7511 (mp) REVERT: B 167 TYR cc_start: 0.8053 (t80) cc_final: 0.7530 (t80) REVERT: B 168 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 179 LEU cc_start: 0.6882 (tp) cc_final: 0.6575 (tp) REVERT: B 181 LEU cc_start: 0.7911 (tp) cc_final: 0.7708 (tp) REVERT: B 186 LEU cc_start: 0.8574 (mt) cc_final: 0.8337 (mt) REVERT: B 192 LYS cc_start: 0.8372 (ptmt) cc_final: 0.8067 (ptmt) REVERT: B 207 ARG cc_start: 0.8766 (ttm170) cc_final: 0.8457 (ttm170) REVERT: B 208 GLU cc_start: 0.7945 (pp20) cc_final: 0.7153 (pp20) REVERT: B 209 ILE cc_start: 0.8830 (mm) cc_final: 0.8573 (mm) REVERT: B 212 ASP cc_start: 0.9001 (m-30) cc_final: 0.8219 (m-30) REVERT: B 214 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8541 (ttpt) REVERT: B 219 TYR cc_start: 0.7325 (p90) cc_final: 0.7107 (p90) REVERT: B 239 LYS cc_start: 0.8632 (mttt) cc_final: 0.8424 (mmtt) REVERT: B 256 PHE cc_start: 0.8389 (p90) cc_final: 0.8078 (p90) REVERT: B 257 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7785 (mtp180) REVERT: B 263 PHE cc_start: 0.8555 (m-80) cc_final: 0.7951 (m-80) REVERT: B 264 GLN cc_start: 0.8570 (tp-100) cc_final: 0.7413 (mt0) REVERT: B 267 PHE cc_start: 0.8078 (m-10) cc_final: 0.7569 (m-10) REVERT: B 291 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7556 (mtt180) REVERT: B 292 LYS cc_start: 0.8731 (pttm) cc_final: 0.8431 (pttm) REVERT: B 299 VAL cc_start: 0.8178 (t) cc_final: 0.7682 (m) REVERT: B 300 MET cc_start: 0.7742 (mmm) cc_final: 0.7317 (mmm) REVERT: B 310 ILE cc_start: 0.8771 (tt) cc_final: 0.8242 (mm) REVERT: B 313 ARG cc_start: 0.8908 (tpt-90) cc_final: 0.8294 (tpp-160) REVERT: B 314 MET cc_start: 0.8409 (tpt) cc_final: 0.7775 (mmm) REVERT: B 315 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8197 (tp40) REVERT: B 316 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8647 (ptpt) REVERT: B 326 MET cc_start: 0.7460 (mmp) cc_final: 0.7051 (mmm) REVERT: B 329 LYS cc_start: 0.7536 (tmtt) cc_final: 0.7196 (tmtt) REVERT: B 345 SER cc_start: 0.7580 (t) cc_final: 0.7232 (p) REVERT: B 351 SER cc_start: 0.8030 (t) cc_final: 0.7728 (p) REVERT: B 353 PHE cc_start: 0.8464 (t80) cc_final: 0.7765 (t80) REVERT: B 356 MET cc_start: 0.8515 (mtt) cc_final: 0.8218 (mmm) REVERT: B 365 GLU cc_start: 0.8213 (pt0) cc_final: 0.7979 (pp20) REVERT: B 372 HIS cc_start: 0.7859 (m-70) cc_final: 0.7158 (m90) REVERT: C 16 LEU cc_start: 0.7127 (tp) cc_final: 0.6347 (pp) REVERT: C 50 LYS cc_start: 0.8188 (mttt) cc_final: 0.7897 (mttt) REVERT: C 51 ASP cc_start: 0.8358 (p0) cc_final: 0.7845 (p0) REVERT: C 57 GLU cc_start: 0.8407 (pt0) cc_final: 0.8142 (pt0) REVERT: C 64 ILE cc_start: 0.8548 (mt) cc_final: 0.8322 (tp) REVERT: C 71 ILE cc_start: 0.7456 (mm) cc_final: 0.7023 (tp) REVERT: C 75 ILE cc_start: 0.8040 (pt) cc_final: 0.7795 (mp) REVERT: C 76 ILE cc_start: 0.7303 (mm) cc_final: 0.6997 (mm) REVERT: C 82 MET cc_start: 0.8081 (tpp) cc_final: 0.7020 (tpp) REVERT: C 84 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8991 (ttmm) REVERT: C 87 HIS cc_start: 0.8182 (t70) cc_final: 0.7583 (t-90) REVERT: C 90 PHE cc_start: 0.7780 (m-10) cc_final: 0.7339 (m-80) REVERT: C 91 TYR cc_start: 0.7966 (m-80) cc_final: 0.7507 (m-80) REVERT: C 105 LEU cc_start: 0.8252 (mt) cc_final: 0.8049 (mp) REVERT: C 111 ASN cc_start: 0.8789 (t0) cc_final: 0.8581 (t0) REVERT: C 113 LYS cc_start: 0.8447 (mttp) cc_final: 0.8095 (mttp) REVERT: C 119 MET cc_start: 0.8476 (ttm) cc_final: 0.8183 (ttm) REVERT: C 121 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8691 (tm-30) REVERT: C 123 MET cc_start: 0.8256 (tpp) cc_final: 0.7243 (tpp) REVERT: C 127 PHE cc_start: 0.7916 (m-80) cc_final: 0.7020 (m-80) REVERT: C 134 VAL cc_start: 0.8338 (t) cc_final: 0.7733 (t) REVERT: C 140 LEU cc_start: 0.8809 (mt) cc_final: 0.8583 (mt) REVERT: C 142 LEU cc_start: 0.8533 (tp) cc_final: 0.8309 (tp) REVERT: C 153 LEU cc_start: 0.8254 (tp) cc_final: 0.7707 (pp) REVERT: C 157 ASP cc_start: 0.7161 (t0) cc_final: 0.6934 (t0) REVERT: C 161 HIS cc_start: 0.6956 (p-80) cc_final: 0.6603 (p-80) REVERT: C 167 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8163 (mm-30) REVERT: C 178 LEU cc_start: 0.7799 (tp) cc_final: 0.7581 (tp) REVERT: C 187 ASP cc_start: 0.8937 (m-30) cc_final: 0.8680 (m-30) REVERT: C 191 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8708 (mtpp) REVERT: C 205 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7627 (mt-10) REVERT: C 211 ASP cc_start: 0.8721 (m-30) cc_final: 0.7693 (m-30) REVERT: C 215 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8580 (mmmm) REVERT: C 216 LEU cc_start: 0.8507 (mt) cc_final: 0.8255 (mp) REVERT: C 242 LEU cc_start: 0.8763 (mt) cc_final: 0.7963 (mp) REVERT: C 252 ASN cc_start: 0.8153 (p0) cc_final: 0.7710 (p0) REVERT: C 253 GLU cc_start: 0.8377 (mp0) cc_final: 0.7869 (mp0) REVERT: C 256 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8022 (mtp180) REVERT: C 259 GLU cc_start: 0.8823 (tp30) cc_final: 0.7930 (tm-30) REVERT: C 262 PHE cc_start: 0.8767 (m-10) cc_final: 0.8494 (m-10) REVERT: C 263 GLN cc_start: 0.8029 (mt0) cc_final: 0.7671 (mt0) REVERT: C 276 GLU cc_start: 0.8462 (tp30) cc_final: 0.7890 (tp30) REVERT: C 279 TYR cc_start: 0.8581 (t80) cc_final: 0.8271 (t80) REVERT: C 280 ASN cc_start: 0.8612 (m110) cc_final: 0.8070 (m110) REVERT: C 282 ILE cc_start: 0.8703 (mt) cc_final: 0.8474 (mt) REVERT: C 283 MET cc_start: 0.8354 (mmm) cc_final: 0.7910 (mmm) REVERT: C 284 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8418 (mtpp) REVERT: C 286 ASP cc_start: 0.8238 (t0) cc_final: 0.7717 (t70) REVERT: C 294 TYR cc_start: 0.8024 (m-80) cc_final: 0.7687 (m-80) REVERT: C 296 ASN cc_start: 0.7287 (p0) cc_final: 0.6591 (p0) REVERT: C 299 MET cc_start: 0.8052 (mmm) cc_final: 0.6511 (mmm) REVERT: C 305 MET cc_start: 0.6735 (mmm) cc_final: 0.6317 (mmm) REVERT: C 314 GLN cc_start: 0.8525 (tt0) cc_final: 0.8129 (mt0) REVERT: C 316 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8006 (mm-30) REVERT: C 327 ILE cc_start: 0.8574 (mm) cc_final: 0.8296 (pt) REVERT: C 329 ILE cc_start: 0.8643 (mm) cc_final: 0.7973 (mt) REVERT: C 356 TRP cc_start: 0.7052 (m100) cc_final: 0.6569 (m100) REVERT: C 361 GLU cc_start: 0.8696 (tp30) cc_final: 0.8111 (tp30) REVERT: C 371 HIS cc_start: 0.6498 (m-70) cc_final: 0.5373 (m-70) REVERT: D 37 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7308 (tpp80) REVERT: D 51 ASP cc_start: 0.7022 (p0) cc_final: 0.5746 (p0) REVERT: D 52 SER cc_start: 0.7608 (t) cc_final: 0.6673 (m) REVERT: D 57 GLU cc_start: 0.8299 (tt0) cc_final: 0.7917 (tp30) REVERT: D 61 LYS cc_start: 0.7939 (mttm) cc_final: 0.7178 (mttt) REVERT: D 62 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7974 (mtm-85) REVERT: D 64 ILE cc_start: 0.8050 (tp) cc_final: 0.7345 (tp) REVERT: D 68 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7421 (mmtt) REVERT: D 72 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 94 LEU cc_start: 0.8132 (mt) cc_final: 0.7859 (mt) REVERT: D 103 THR cc_start: 0.7855 (m) cc_final: 0.7628 (t) REVERT: D 111 ASN cc_start: 0.8009 (m-40) cc_final: 0.6930 (m-40) REVERT: D 117 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 119 MET cc_start: 0.8976 (ttm) cc_final: 0.8745 (ttm) REVERT: D 121 GLN cc_start: 0.8613 (pp30) cc_final: 0.8262 (pp30) REVERT: D 124 PHE cc_start: 0.7861 (m-80) cc_final: 0.7159 (m-80) REVERT: D 132 MET cc_start: 0.6831 (mmp) cc_final: 0.6213 (mmp) REVERT: D 133 TYR cc_start: 0.7552 (t80) cc_final: 0.7164 (t80) REVERT: D 137 GLN cc_start: 0.8019 (mt0) cc_final: 0.7637 (mt0) REVERT: D 139 VAL cc_start: 0.8562 (m) cc_final: 0.8147 (p) REVERT: D 151 ILE cc_start: 0.8099 (tt) cc_final: 0.7771 (tt) REVERT: D 165 ILE cc_start: 0.7844 (mt) cc_final: 0.7583 (tt) REVERT: D 176 MET cc_start: 0.7028 (mmm) cc_final: 0.6747 (mmm) REVERT: D 178 LEU cc_start: 0.8319 (tp) cc_final: 0.8087 (tp) REVERT: D 196 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7757 (tpp80) REVERT: D 205 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8393 (mt-10) REVERT: D 207 GLU cc_start: 0.8118 (mm-30) cc_final: 0.6744 (mm-30) REVERT: D 211 ASP cc_start: 0.8724 (m-30) cc_final: 0.7405 (m-30) REVERT: D 213 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8477 (ttpt) REVERT: D 214 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7879 (mt-10) REVERT: D 238 LYS cc_start: 0.7349 (mttp) cc_final: 0.6948 (mmtp) REVERT: D 240 TYR cc_start: 0.8039 (t80) cc_final: 0.7807 (t80) REVERT: D 241 GLU cc_start: 0.7975 (pp20) cc_final: 0.7672 (pp20) REVERT: D 259 GLU cc_start: 0.8598 (tp30) cc_final: 0.8155 (tp30) REVERT: D 283 MET cc_start: 0.8474 (mmp) cc_final: 0.8177 (mmp) REVERT: D 286 ASP cc_start: 0.8405 (t0) cc_final: 0.7967 (t0) REVERT: D 288 ASP cc_start: 0.8690 (m-30) cc_final: 0.8081 (m-30) REVERT: D 290 ARG cc_start: 0.8081 (mtt180) cc_final: 0.6976 (mtt180) REVERT: D 292 ASP cc_start: 0.8542 (m-30) cc_final: 0.8254 (m-30) REVERT: D 294 TYR cc_start: 0.8344 (m-80) cc_final: 0.7765 (m-80) REVERT: D 297 ASN cc_start: 0.7773 (m-40) cc_final: 0.7529 (m-40) REVERT: D 299 MET cc_start: 0.8239 (mmm) cc_final: 0.7720 (mmm) REVERT: D 303 THR cc_start: 0.8011 (m) cc_final: 0.7692 (p) REVERT: D 312 ARG cc_start: 0.8934 (tpt-90) cc_final: 0.8517 (tpt-90) REVERT: D 314 GLN cc_start: 0.9076 (tt0) cc_final: 0.8860 (mt0) outliers start: 3 outliers final: 0 residues processed: 769 average time/residue: 0.3198 time to fit residues: 341.5516 Evaluate side-chains 707 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 705 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 8.9990 chunk 173 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 656 HIS ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN B 174 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.114066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087765 restraints weight = 42259.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091578 restraints weight = 25448.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094244 restraints weight = 17278.677| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15177 Z= 0.195 Angle : 0.622 6.920 20547 Z= 0.316 Chirality : 0.043 0.159 2251 Planarity : 0.005 0.062 2631 Dihedral : 9.303 163.464 2071 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1847 helix: 0.99 (0.18), residues: 843 sheet: -1.39 (0.28), residues: 307 loop : 0.10 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 340 HIS 0.004 0.001 HIS A 430 PHE 0.019 0.001 PHE D 352 TYR 0.029 0.001 TYR A 439 ARG 0.008 0.001 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 761 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7299 (mm-30) REVERT: A 89 LEU cc_start: 0.8356 (mt) cc_final: 0.8022 (pp) REVERT: A 92 ARG cc_start: 0.8197 (mmp-170) cc_final: 0.7346 (mmm160) REVERT: A 99 ILE cc_start: 0.8081 (pt) cc_final: 0.7721 (pt) REVERT: A 103 CYS cc_start: 0.6417 (t) cc_final: 0.6017 (t) REVERT: A 107 LEU cc_start: 0.7088 (tp) cc_final: 0.6759 (tp) REVERT: A 110 ILE cc_start: 0.7444 (mp) cc_final: 0.6967 (tp) REVERT: A 121 GLU cc_start: 0.8618 (pm20) cc_final: 0.8351 (tp30) REVERT: A 122 ASP cc_start: 0.9087 (m-30) cc_final: 0.8758 (p0) REVERT: A 130 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8473 (mm110) REVERT: A 138 HIS cc_start: 0.6414 (t-90) cc_final: 0.5273 (t-90) REVERT: A 149 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 150 MET cc_start: 0.8107 (ttp) cc_final: 0.6747 (tpp) REVERT: A 156 ASN cc_start: 0.7246 (p0) cc_final: 0.6875 (p0) REVERT: A 157 GLN cc_start: 0.7523 (mp-120) cc_final: 0.6785 (mm-40) REVERT: A 178 ARG cc_start: 0.8342 (ptt90) cc_final: 0.8114 (ppt170) REVERT: A 179 TYR cc_start: 0.8503 (t80) cc_final: 0.8055 (t80) REVERT: A 194 GLU cc_start: 0.7195 (tp30) cc_final: 0.6952 (tm-30) REVERT: A 220 PHE cc_start: 0.7757 (p90) cc_final: 0.7257 (p90) REVERT: A 239 MET cc_start: 0.7022 (mmp) cc_final: 0.6549 (mmp) REVERT: A 248 ARG cc_start: 0.8351 (tpp80) cc_final: 0.7647 (tpp-160) REVERT: A 259 TYR cc_start: 0.7650 (m-80) cc_final: 0.6615 (m-80) REVERT: A 260 HIS cc_start: 0.8328 (m-70) cc_final: 0.8029 (m-70) REVERT: A 262 PHE cc_start: 0.8698 (m-80) cc_final: 0.8031 (m-80) REVERT: A 286 HIS cc_start: 0.6622 (t70) cc_final: 0.6281 (t-90) REVERT: A 307 HIS cc_start: 0.8863 (m90) cc_final: 0.8561 (m90) REVERT: A 309 ARG cc_start: 0.8784 (ptt90) cc_final: 0.8521 (ptt90) REVERT: A 312 CYS cc_start: 0.8564 (m) cc_final: 0.7937 (m) REVERT: A 315 LEU cc_start: 0.7184 (mt) cc_final: 0.6853 (mt) REVERT: A 317 ILE cc_start: 0.8541 (mt) cc_final: 0.7833 (mt) REVERT: A 322 GLN cc_start: 0.8732 (mt0) cc_final: 0.8459 (mp10) REVERT: A 327 ARG cc_start: 0.8589 (mpt180) cc_final: 0.8249 (mmt-90) REVERT: A 354 HIS cc_start: 0.6833 (t-90) cc_final: 0.6246 (t-90) REVERT: A 370 GLU cc_start: 0.8362 (tt0) cc_final: 0.8064 (tt0) REVERT: A 371 MET cc_start: 0.9059 (mtm) cc_final: 0.8579 (ptm) REVERT: A 373 HIS cc_start: 0.8468 (t70) cc_final: 0.8067 (t70) REVERT: A 408 TYR cc_start: 0.8744 (t80) cc_final: 0.7820 (t80) REVERT: A 419 VAL cc_start: 0.8875 (m) cc_final: 0.8571 (m) REVERT: A 420 ASN cc_start: 0.8249 (t0) cc_final: 0.8040 (m110) REVERT: A 423 LEU cc_start: 0.7454 (mt) cc_final: 0.6980 (mt) REVERT: A 451 GLN cc_start: 0.8745 (mp10) cc_final: 0.8484 (mp10) REVERT: A 452 PHE cc_start: 0.8386 (t80) cc_final: 0.7994 (t80) REVERT: A 468 HIS cc_start: 0.8159 (t-90) cc_final: 0.7688 (t-90) REVERT: A 470 PHE cc_start: 0.8082 (m-80) cc_final: 0.7425 (m-80) REVERT: A 478 MET cc_start: 0.8882 (mtm) cc_final: 0.8539 (mtm) REVERT: A 498 LEU cc_start: 0.9009 (mp) cc_final: 0.8374 (tt) REVERT: A 512 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7368 (mm-30) REVERT: A 515 MET cc_start: 0.7268 (ttm) cc_final: 0.6832 (ttm) REVERT: A 520 ASP cc_start: 0.8423 (p0) cc_final: 0.8131 (m-30) REVERT: A 526 LYS cc_start: 0.9045 (tttt) cc_final: 0.8431 (mmmt) REVERT: A 532 LEU cc_start: 0.7888 (mt) cc_final: 0.7290 (mt) REVERT: A 537 LEU cc_start: 0.8842 (mp) cc_final: 0.8621 (mp) REVERT: A 545 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.7962 (t0) REVERT: A 556 LYS cc_start: 0.8634 (mttt) cc_final: 0.8286 (mmtt) REVERT: A 558 GLU cc_start: 0.7854 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 559 TYR cc_start: 0.7385 (m-80) cc_final: 0.6747 (m-80) REVERT: A 568 ASN cc_start: 0.8246 (t0) cc_final: 0.7806 (t0) REVERT: A 587 MET cc_start: 0.8666 (mmp) cc_final: 0.8367 (mmm) REVERT: A 633 LYS cc_start: 0.7189 (mtmm) cc_final: 0.6912 (mmmm) REVERT: A 637 HIS cc_start: 0.8362 (t-90) cc_final: 0.7194 (t-90) REVERT: A 638 GLN cc_start: 0.8981 (tt0) cc_final: 0.8701 (pt0) REVERT: A 640 ARG cc_start: 0.8970 (ptp-170) cc_final: 0.8340 (ptm-80) REVERT: A 641 ASN cc_start: 0.9099 (m110) cc_final: 0.8439 (m110) REVERT: A 643 LEU cc_start: 0.8627 (tp) cc_final: 0.7412 (tp) REVERT: A 644 HIS cc_start: 0.8404 (m90) cc_final: 0.8013 (m90) REVERT: A 647 MET cc_start: 0.8633 (mmm) cc_final: 0.7838 (mmm) REVERT: A 648 GLU cc_start: 0.8811 (tp30) cc_final: 0.8435 (tm-30) REVERT: A 649 THR cc_start: 0.9104 (p) cc_final: 0.8650 (p) REVERT: A 657 TYR cc_start: 0.6658 (m-80) cc_final: 0.6024 (m-80) REVERT: A 666 PHE cc_start: 0.8338 (m-10) cc_final: 0.8074 (m-10) REVERT: A 687 LEU cc_start: 0.8791 (pp) cc_final: 0.8414 (pp) REVERT: A 757 TYR cc_start: 0.8929 (t80) cc_final: 0.8573 (t80) REVERT: B 51 LYS cc_start: 0.8451 (mppt) cc_final: 0.8119 (ttpp) REVERT: B 62 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8087 (mmtm) REVERT: B 76 ILE cc_start: 0.8537 (pt) cc_final: 0.8322 (pt) REVERT: B 83 MET cc_start: 0.8331 (tpp) cc_final: 0.7671 (tpp) REVERT: B 84 GLU cc_start: 0.8798 (tt0) cc_final: 0.8399 (tm-30) REVERT: B 85 LYS cc_start: 0.9164 (mttm) cc_final: 0.8866 (mttm) REVERT: B 93 ASN cc_start: 0.8181 (m110) cc_final: 0.7842 (m110) REVERT: B 106 LEU cc_start: 0.7895 (mt) cc_final: 0.6949 (mt) REVERT: B 111 LEU cc_start: 0.8333 (mt) cc_final: 0.7431 (mt) REVERT: B 114 LYS cc_start: 0.8503 (ptmm) cc_final: 0.7690 (ptmm) REVERT: B 119 LYS cc_start: 0.8324 (tppt) cc_final: 0.7481 (tppt) REVERT: B 120 MET cc_start: 0.8498 (ttm) cc_final: 0.7817 (tmm) REVERT: B 122 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8046 (tm-30) REVERT: B 123 ILE cc_start: 0.8477 (mt) cc_final: 0.7844 (mt) REVERT: B 124 MET cc_start: 0.8373 (tpp) cc_final: 0.7747 (tpp) REVERT: B 128 PHE cc_start: 0.8182 (m-80) cc_final: 0.7321 (m-80) REVERT: B 133 MET cc_start: 0.7411 (ttp) cc_final: 0.6715 (ttp) REVERT: B 134 TYR cc_start: 0.7350 (t80) cc_final: 0.7050 (t80) REVERT: B 155 ASP cc_start: 0.6724 (t0) cc_final: 0.6246 (t0) REVERT: B 167 TYR cc_start: 0.8055 (t80) cc_final: 0.7439 (t80) REVERT: B 168 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 179 LEU cc_start: 0.6857 (tp) cc_final: 0.6520 (tp) REVERT: B 186 LEU cc_start: 0.8614 (mt) cc_final: 0.8361 (mt) REVERT: B 192 LYS cc_start: 0.8300 (ptmt) cc_final: 0.7949 (ptmt) REVERT: B 207 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8466 (ttm170) REVERT: B 208 GLU cc_start: 0.8066 (pp20) cc_final: 0.7672 (pm20) REVERT: B 214 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8495 (ttpt) REVERT: B 216 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8521 (mmmm) REVERT: B 219 TYR cc_start: 0.7341 (p90) cc_final: 0.7065 (p90) REVERT: B 226 ASN cc_start: 0.8689 (t0) cc_final: 0.8139 (t0) REVERT: B 239 LYS cc_start: 0.8561 (mttt) cc_final: 0.8312 (mmtt) REVERT: B 257 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7752 (mtp180) REVERT: B 260 GLU cc_start: 0.8259 (tp30) cc_final: 0.8055 (tp30) REVERT: B 263 PHE cc_start: 0.8600 (m-80) cc_final: 0.7786 (m-80) REVERT: B 264 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7448 (mt0) REVERT: B 267 PHE cc_start: 0.8195 (m-10) cc_final: 0.7614 (m-10) REVERT: B 277 GLU cc_start: 0.8520 (tp30) cc_final: 0.8300 (tp30) REVERT: B 292 LYS cc_start: 0.8700 (pttm) cc_final: 0.8389 (pttm) REVERT: B 293 ASP cc_start: 0.8743 (m-30) cc_final: 0.8479 (m-30) REVERT: B 300 MET cc_start: 0.7914 (mmm) cc_final: 0.7596 (mmm) REVERT: B 306 MET cc_start: 0.7265 (mmt) cc_final: 0.7001 (mmt) REVERT: B 310 ILE cc_start: 0.8770 (tt) cc_final: 0.8288 (pt) REVERT: B 313 ARG cc_start: 0.8855 (tpt-90) cc_final: 0.8196 (tpp-160) REVERT: B 314 MET cc_start: 0.8390 (tpt) cc_final: 0.7856 (mmm) REVERT: B 316 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8596 (ptpt) REVERT: B 326 MET cc_start: 0.7391 (mmp) cc_final: 0.7030 (mmm) REVERT: B 329 LYS cc_start: 0.7436 (tmtt) cc_final: 0.7150 (tmtt) REVERT: B 335 GLU cc_start: 0.8118 (mp0) cc_final: 0.7792 (mm-30) REVERT: B 338 TYR cc_start: 0.7874 (m-80) cc_final: 0.7330 (m-80) REVERT: B 351 SER cc_start: 0.8021 (t) cc_final: 0.7665 (p) REVERT: B 353 PHE cc_start: 0.8468 (t80) cc_final: 0.7767 (t80) REVERT: B 355 GLN cc_start: 0.8768 (pp30) cc_final: 0.8544 (pp30) REVERT: B 356 MET cc_start: 0.8450 (mtt) cc_final: 0.8184 (mmm) REVERT: B 365 GLU cc_start: 0.8257 (pt0) cc_final: 0.8053 (pp20) REVERT: B 372 HIS cc_start: 0.7768 (m-70) cc_final: 0.7082 (m90) REVERT: C 51 ASP cc_start: 0.8533 (p0) cc_final: 0.8287 (p0) REVERT: C 57 GLU cc_start: 0.8459 (pt0) cc_final: 0.8216 (pt0) REVERT: C 61 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8283 (mmtm) REVERT: C 71 ILE cc_start: 0.7351 (mm) cc_final: 0.6903 (tp) REVERT: C 75 ILE cc_start: 0.8065 (pt) cc_final: 0.7754 (mp) REVERT: C 82 MET cc_start: 0.8005 (tpp) cc_final: 0.6948 (tpp) REVERT: C 84 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8747 (ttmm) REVERT: C 87 HIS cc_start: 0.8239 (t70) cc_final: 0.7582 (t-90) REVERT: C 90 PHE cc_start: 0.7699 (m-10) cc_final: 0.7244 (m-80) REVERT: C 91 TYR cc_start: 0.7960 (m-80) cc_final: 0.7525 (m-80) REVERT: C 107 GLU cc_start: 0.6996 (pm20) cc_final: 0.6656 (pm20) REVERT: C 111 ASN cc_start: 0.8880 (t0) cc_final: 0.8624 (t0) REVERT: C 113 LYS cc_start: 0.8311 (mttp) cc_final: 0.8024 (mttp) REVERT: C 117 GLU cc_start: 0.8414 (pp20) cc_final: 0.8185 (pp20) REVERT: C 121 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8709 (tm-30) REVERT: C 123 MET cc_start: 0.8176 (tpp) cc_final: 0.7248 (tpp) REVERT: C 127 PHE cc_start: 0.7463 (m-80) cc_final: 0.6990 (m-80) REVERT: C 161 HIS cc_start: 0.6563 (p-80) cc_final: 0.6272 (p-80) REVERT: C 178 LEU cc_start: 0.7853 (tp) cc_final: 0.7646 (tp) REVERT: C 187 ASP cc_start: 0.8892 (m-30) cc_final: 0.8681 (m-30) REVERT: C 191 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8730 (mtpp) REVERT: C 205 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 207 GLU cc_start: 0.7974 (pp20) cc_final: 0.7576 (pp20) REVERT: C 210 ARG cc_start: 0.8778 (tmm-80) cc_final: 0.8568 (ttp80) REVERT: C 211 ASP cc_start: 0.8837 (m-30) cc_final: 0.7812 (m-30) REVERT: C 218 TYR cc_start: 0.6026 (p90) cc_final: 0.5317 (p90) REVERT: C 248 ILE cc_start: 0.8810 (pt) cc_final: 0.8188 (mm) REVERT: C 253 GLU cc_start: 0.8297 (mp0) cc_final: 0.8069 (mp0) REVERT: C 259 GLU cc_start: 0.8878 (tp30) cc_final: 0.8010 (tm-30) REVERT: C 263 GLN cc_start: 0.8010 (mt0) cc_final: 0.7549 (mt0) REVERT: C 276 GLU cc_start: 0.8484 (tp30) cc_final: 0.7669 (tp30) REVERT: C 279 TYR cc_start: 0.8516 (t80) cc_final: 0.8299 (t80) REVERT: C 280 ASN cc_start: 0.8672 (m110) cc_final: 0.7946 (m-40) REVERT: C 282 ILE cc_start: 0.8720 (mt) cc_final: 0.8455 (mt) REVERT: C 283 MET cc_start: 0.8309 (mmm) cc_final: 0.7857 (mmm) REVERT: C 284 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8434 (mtpp) REVERT: C 286 ASP cc_start: 0.8469 (t0) cc_final: 0.7822 (t70) REVERT: C 294 TYR cc_start: 0.7972 (m-80) cc_final: 0.7629 (m-80) REVERT: C 296 ASN cc_start: 0.7289 (p0) cc_final: 0.6721 (p0) REVERT: C 299 MET cc_start: 0.7969 (mmm) cc_final: 0.7571 (mmm) REVERT: C 313 MET cc_start: 0.8263 (tpp) cc_final: 0.7351 (tpp) REVERT: C 314 GLN cc_start: 0.8527 (tt0) cc_final: 0.8098 (mt0) REVERT: C 327 ILE cc_start: 0.8600 (mm) cc_final: 0.8236 (pt) REVERT: C 328 LYS cc_start: 0.8456 (mttp) cc_final: 0.8185 (mttp) REVERT: C 329 ILE cc_start: 0.8587 (mm) cc_final: 0.7990 (mm) REVERT: C 356 TRP cc_start: 0.6850 (m100) cc_final: 0.6202 (m100) REVERT: C 361 GLU cc_start: 0.8643 (tp30) cc_final: 0.8071 (tp30) REVERT: D 8 LEU cc_start: 0.7901 (mt) cc_final: 0.7697 (mt) REVERT: D 37 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7374 (tpp80) REVERT: D 41 GLN cc_start: 0.8146 (tp40) cc_final: 0.7574 (tm-30) REVERT: D 44 MET cc_start: 0.6239 (mtp) cc_final: 0.6015 (mtp) REVERT: D 47 MET cc_start: 0.5678 (mmp) cc_final: 0.5416 (tmm) REVERT: D 50 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7482 (mtmm) REVERT: D 52 SER cc_start: 0.7779 (t) cc_final: 0.6951 (m) REVERT: D 62 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7773 (mtm-85) REVERT: D 64 ILE cc_start: 0.8104 (tp) cc_final: 0.7474 (tt) REVERT: D 65 LEU cc_start: 0.8573 (mt) cc_final: 0.8362 (mt) REVERT: D 68 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7471 (mmtt) REVERT: D 81 ASP cc_start: 0.8222 (m-30) cc_final: 0.7434 (m-30) REVERT: D 84 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8619 (mtmt) REVERT: D 94 LEU cc_start: 0.8196 (mt) cc_final: 0.7936 (mt) REVERT: D 105 LEU cc_start: 0.7776 (mm) cc_final: 0.7058 (mm) REVERT: D 107 GLU cc_start: 0.6837 (pt0) cc_final: 0.5839 (pt0) REVERT: D 111 ASN cc_start: 0.8317 (m-40) cc_final: 0.6610 (m-40) REVERT: D 117 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 119 MET cc_start: 0.8899 (ttm) cc_final: 0.8590 (ttm) REVERT: D 121 GLN cc_start: 0.8630 (pp30) cc_final: 0.8248 (pp30) REVERT: D 124 PHE cc_start: 0.7891 (m-80) cc_final: 0.7215 (m-80) REVERT: D 127 PHE cc_start: 0.8302 (m-10) cc_final: 0.7991 (m-10) REVERT: D 132 MET cc_start: 0.6840 (mmp) cc_final: 0.6310 (mmp) REVERT: D 137 GLN cc_start: 0.8041 (mt0) cc_final: 0.7665 (mt0) REVERT: D 139 VAL cc_start: 0.8482 (m) cc_final: 0.8073 (p) REVERT: D 165 ILE cc_start: 0.7902 (mt) cc_final: 0.7620 (tt) REVERT: D 166 TYR cc_start: 0.7514 (t80) cc_final: 0.7161 (t80) REVERT: D 167 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 176 MET cc_start: 0.7015 (mmm) cc_final: 0.6734 (mmm) REVERT: D 187 ASP cc_start: 0.8790 (m-30) cc_final: 0.8474 (m-30) REVERT: D 196 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7638 (tpp80) REVERT: D 205 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8367 (mt-10) REVERT: D 210 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7466 (ttp80) REVERT: D 211 ASP cc_start: 0.8524 (m-30) cc_final: 0.8041 (m-30) REVERT: D 213 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8481 (ttpt) REVERT: D 214 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7896 (mt-10) REVERT: D 240 TYR cc_start: 0.8022 (t80) cc_final: 0.7733 (t80) REVERT: D 259 GLU cc_start: 0.8523 (tp30) cc_final: 0.8120 (tp30) REVERT: D 283 MET cc_start: 0.8560 (mmp) cc_final: 0.8331 (mmp) REVERT: D 286 ASP cc_start: 0.8361 (t0) cc_final: 0.7822 (t0) REVERT: D 288 ASP cc_start: 0.8614 (m-30) cc_final: 0.7813 (m-30) REVERT: D 289 ILE cc_start: 0.7968 (pt) cc_final: 0.7477 (mm) REVERT: D 290 ARG cc_start: 0.7955 (mtt180) cc_final: 0.6800 (mtt90) REVERT: D 292 ASP cc_start: 0.8487 (m-30) cc_final: 0.8271 (m-30) REVERT: D 294 TYR cc_start: 0.8231 (m-80) cc_final: 0.7563 (m-80) REVERT: D 297 ASN cc_start: 0.7903 (m-40) cc_final: 0.7647 (m-40) REVERT: D 299 MET cc_start: 0.8193 (mmm) cc_final: 0.7715 (mmm) REVERT: D 312 ARG cc_start: 0.8928 (tpt-90) cc_final: 0.8110 (tpt-90) REVERT: D 313 MET cc_start: 0.8459 (tpp) cc_final: 0.8047 (tpp) REVERT: D 314 GLN cc_start: 0.9038 (tt0) cc_final: 0.8661 (mm-40) REVERT: D 316 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8124 (mt-10) REVERT: D 320 LEU cc_start: 0.8872 (mt) cc_final: 0.8672 (mt) REVERT: D 328 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8199 (mmtt) outliers start: 1 outliers final: 0 residues processed: 761 average time/residue: 0.3200 time to fit residues: 337.0236 Evaluate side-chains 702 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 701 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 32 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 184 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 ASN B 174 HIS B 354 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.114191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088049 restraints weight = 42621.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091885 restraints weight = 25429.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094611 restraints weight = 17160.821| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15177 Z= 0.186 Angle : 0.631 7.532 20547 Z= 0.321 Chirality : 0.044 0.208 2251 Planarity : 0.005 0.086 2631 Dihedral : 9.111 166.366 2071 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1847 helix: 1.10 (0.18), residues: 834 sheet: -1.27 (0.28), residues: 305 loop : 0.06 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 80 HIS 0.005 0.001 HIS D 101 PHE 0.017 0.001 PHE B 125 TYR 0.036 0.002 TYR A 477 ARG 0.020 0.001 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 753 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7326 (mm-30) REVERT: A 79 TYR cc_start: 0.7708 (m-80) cc_final: 0.7384 (m-80) REVERT: A 92 ARG cc_start: 0.8230 (mmp-170) cc_final: 0.7369 (mmm160) REVERT: A 99 ILE cc_start: 0.8060 (pt) cc_final: 0.7671 (pt) REVERT: A 101 THR cc_start: 0.7870 (m) cc_final: 0.7635 (m) REVERT: A 110 ILE cc_start: 0.7475 (mp) cc_final: 0.7030 (tp) REVERT: A 121 GLU cc_start: 0.8611 (pm20) cc_final: 0.8380 (tp30) REVERT: A 130 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8353 (mm110) REVERT: A 138 HIS cc_start: 0.6339 (t-90) cc_final: 0.5175 (t-90) REVERT: A 149 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8286 (mm-40) REVERT: A 150 MET cc_start: 0.8244 (ttp) cc_final: 0.7793 (ttp) REVERT: A 174 LYS cc_start: 0.8908 (pttp) cc_final: 0.8569 (pttm) REVERT: A 179 TYR cc_start: 0.8347 (t80) cc_final: 0.7924 (t80) REVERT: A 220 PHE cc_start: 0.7757 (p90) cc_final: 0.7150 (p90) REVERT: A 239 MET cc_start: 0.6904 (mmp) cc_final: 0.6313 (mmp) REVERT: A 240 ARG cc_start: 0.7635 (mtp85) cc_final: 0.6899 (mtp85) REVERT: A 242 TYR cc_start: 0.7076 (m-80) cc_final: 0.6781 (m-80) REVERT: A 248 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7776 (tpp-160) REVERT: A 259 TYR cc_start: 0.7691 (m-80) cc_final: 0.6768 (m-80) REVERT: A 260 HIS cc_start: 0.8330 (m-70) cc_final: 0.8128 (m-70) REVERT: A 262 PHE cc_start: 0.8604 (m-80) cc_final: 0.7940 (m-80) REVERT: A 286 HIS cc_start: 0.6791 (t70) cc_final: 0.6393 (t-90) REVERT: A 307 HIS cc_start: 0.8833 (m90) cc_final: 0.8508 (m90) REVERT: A 309 ARG cc_start: 0.8883 (ppt170) cc_final: 0.8352 (ptt90) REVERT: A 312 CYS cc_start: 0.8579 (m) cc_final: 0.7972 (m) REVERT: A 317 ILE cc_start: 0.8549 (mt) cc_final: 0.7874 (mt) REVERT: A 322 GLN cc_start: 0.8761 (mt0) cc_final: 0.8499 (mp10) REVERT: A 327 ARG cc_start: 0.8585 (mpt180) cc_final: 0.8205 (mmt180) REVERT: A 364 MET cc_start: 0.7829 (mtt) cc_final: 0.7545 (mtt) REVERT: A 370 GLU cc_start: 0.8340 (tt0) cc_final: 0.8073 (tt0) REVERT: A 371 MET cc_start: 0.8993 (mtm) cc_final: 0.8527 (ptm) REVERT: A 373 HIS cc_start: 0.8464 (t70) cc_final: 0.8071 (t70) REVERT: A 408 TYR cc_start: 0.8764 (t80) cc_final: 0.7846 (t80) REVERT: A 419 VAL cc_start: 0.8891 (m) cc_final: 0.8592 (m) REVERT: A 423 LEU cc_start: 0.7568 (mt) cc_final: 0.7047 (mt) REVERT: A 451 GLN cc_start: 0.8734 (mp10) cc_final: 0.8380 (mp10) REVERT: A 452 PHE cc_start: 0.8488 (t80) cc_final: 0.7995 (t80) REVERT: A 453 CYS cc_start: 0.8721 (p) cc_final: 0.8515 (p) REVERT: A 463 GLN cc_start: 0.8846 (tt0) cc_final: 0.8243 (mm-40) REVERT: A 468 HIS cc_start: 0.8215 (t-90) cc_final: 0.7618 (t-90) REVERT: A 470 PHE cc_start: 0.8151 (m-80) cc_final: 0.7814 (m-80) REVERT: A 475 GLU cc_start: 0.8481 (pp20) cc_final: 0.8267 (pp20) REVERT: A 478 MET cc_start: 0.8796 (mtm) cc_final: 0.8399 (mtm) REVERT: A 493 GLN cc_start: 0.8728 (tp-100) cc_final: 0.7831 (tp-100) REVERT: A 498 LEU cc_start: 0.9019 (mp) cc_final: 0.8385 (tt) REVERT: A 511 GLU cc_start: 0.8646 (tp30) cc_final: 0.8184 (tp30) REVERT: A 512 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 515 MET cc_start: 0.7184 (ttm) cc_final: 0.6404 (ttm) REVERT: A 520 ASP cc_start: 0.8457 (p0) cc_final: 0.8218 (m-30) REVERT: A 525 GLN cc_start: 0.8476 (tp40) cc_final: 0.7419 (tp-100) REVERT: A 526 LYS cc_start: 0.9057 (tttt) cc_final: 0.8333 (mmmt) REVERT: A 529 ASN cc_start: 0.8557 (m-40) cc_final: 0.7507 (m-40) REVERT: A 532 LEU cc_start: 0.7937 (mt) cc_final: 0.7159 (mt) REVERT: A 537 LEU cc_start: 0.9004 (mp) cc_final: 0.8743 (mp) REVERT: A 538 PHE cc_start: 0.8085 (t80) cc_final: 0.7427 (t80) REVERT: A 545 ASN cc_start: 0.8208 (t0) cc_final: 0.7994 (t0) REVERT: A 556 LYS cc_start: 0.8632 (mttt) cc_final: 0.8126 (mttm) REVERT: A 558 GLU cc_start: 0.7860 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 559 TYR cc_start: 0.7304 (m-80) cc_final: 0.6783 (m-80) REVERT: A 568 ASN cc_start: 0.8263 (t0) cc_final: 0.7863 (t0) REVERT: A 574 GLU cc_start: 0.8659 (tp30) cc_final: 0.8150 (pm20) REVERT: A 633 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6692 (mmtt) REVERT: A 637 HIS cc_start: 0.8048 (t-90) cc_final: 0.7587 (t-90) REVERT: A 638 GLN cc_start: 0.8875 (tt0) cc_final: 0.8613 (pt0) REVERT: A 640 ARG cc_start: 0.8977 (ptp-170) cc_final: 0.8283 (ptm-80) REVERT: A 641 ASN cc_start: 0.9027 (m110) cc_final: 0.8662 (m-40) REVERT: A 643 LEU cc_start: 0.8640 (tp) cc_final: 0.7467 (tp) REVERT: A 644 HIS cc_start: 0.8428 (m90) cc_final: 0.7980 (m90) REVERT: A 647 MET cc_start: 0.8616 (mmm) cc_final: 0.7877 (mmm) REVERT: A 648 GLU cc_start: 0.8787 (tp30) cc_final: 0.8379 (tm-30) REVERT: A 649 THR cc_start: 0.9042 (p) cc_final: 0.8628 (p) REVERT: A 657 TYR cc_start: 0.6755 (m-80) cc_final: 0.6325 (m-80) REVERT: A 666 PHE cc_start: 0.8381 (m-10) cc_final: 0.8008 (m-10) REVERT: A 676 ARG cc_start: 0.8608 (mmp80) cc_final: 0.7605 (ttm110) REVERT: A 750 PHE cc_start: 0.9019 (m-10) cc_final: 0.8782 (m-10) REVERT: A 757 TYR cc_start: 0.8942 (t80) cc_final: 0.8569 (t80) REVERT: B 35 ILE cc_start: 0.8429 (mt) cc_final: 0.7924 (tp) REVERT: B 48 MET cc_start: 0.7111 (mmt) cc_final: 0.6475 (tpp) REVERT: B 77 ILE cc_start: 0.8659 (mm) cc_final: 0.8380 (tt) REVERT: B 83 MET cc_start: 0.8322 (tpp) cc_final: 0.7704 (tpp) REVERT: B 84 GLU cc_start: 0.8796 (tt0) cc_final: 0.8380 (tm-30) REVERT: B 85 LYS cc_start: 0.9184 (mttm) cc_final: 0.8881 (mttm) REVERT: B 106 LEU cc_start: 0.7962 (mt) cc_final: 0.7727 (mt) REVERT: B 114 LYS cc_start: 0.8497 (ptmm) cc_final: 0.7614 (ptmm) REVERT: B 120 MET cc_start: 0.8525 (ttm) cc_final: 0.7778 (tmm) REVERT: B 121 THR cc_start: 0.8592 (p) cc_final: 0.7963 (p) REVERT: B 124 MET cc_start: 0.8294 (tpp) cc_final: 0.7732 (tpp) REVERT: B 128 PHE cc_start: 0.8083 (m-80) cc_final: 0.7239 (m-10) REVERT: B 133 MET cc_start: 0.7484 (ttp) cc_final: 0.6751 (ttp) REVERT: B 134 TYR cc_start: 0.7243 (t80) cc_final: 0.7032 (t80) REVERT: B 137 ILE cc_start: 0.7931 (tt) cc_final: 0.7683 (tp) REVERT: B 144 TYR cc_start: 0.8437 (m-80) cc_final: 0.8233 (m-80) REVERT: B 155 ASP cc_start: 0.6756 (t0) cc_final: 0.6294 (t0) REVERT: B 167 TYR cc_start: 0.8033 (t80) cc_final: 0.7513 (t80) REVERT: B 168 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 178 ARG cc_start: 0.7137 (ttm-80) cc_final: 0.6524 (ttm-80) REVERT: B 179 LEU cc_start: 0.6760 (tp) cc_final: 0.6414 (tp) REVERT: B 186 LEU cc_start: 0.8594 (mt) cc_final: 0.8343 (mt) REVERT: B 192 LYS cc_start: 0.8354 (ptmt) cc_final: 0.8014 (ptmt) REVERT: B 193 ILE cc_start: 0.8870 (pt) cc_final: 0.8320 (tt) REVERT: B 207 ARG cc_start: 0.8769 (ttm170) cc_final: 0.8124 (ttm-80) REVERT: B 212 ASP cc_start: 0.8969 (m-30) cc_final: 0.7902 (m-30) REVERT: B 214 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8546 (ttpt) REVERT: B 216 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8582 (mmmm) REVERT: B 219 TYR cc_start: 0.7434 (p90) cc_final: 0.7176 (p90) REVERT: B 226 ASN cc_start: 0.8460 (t0) cc_final: 0.8218 (t0) REVERT: B 239 LYS cc_start: 0.8566 (mttt) cc_final: 0.8250 (mmtt) REVERT: B 256 PHE cc_start: 0.8423 (p90) cc_final: 0.8151 (p90) REVERT: B 263 PHE cc_start: 0.8622 (m-80) cc_final: 0.7833 (m-80) REVERT: B 264 GLN cc_start: 0.8599 (tp-100) cc_final: 0.7308 (mt0) REVERT: B 267 PHE cc_start: 0.8213 (m-10) cc_final: 0.7563 (m-10) REVERT: B 280 TYR cc_start: 0.7938 (t80) cc_final: 0.7581 (t80) REVERT: B 291 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7756 (mtt-85) REVERT: B 292 LYS cc_start: 0.8685 (pttm) cc_final: 0.8367 (pttm) REVERT: B 293 ASP cc_start: 0.8777 (m-30) cc_final: 0.8511 (m-30) REVERT: B 298 ASN cc_start: 0.7144 (m-40) cc_final: 0.6576 (m-40) REVERT: B 300 MET cc_start: 0.7914 (mmm) cc_final: 0.7661 (mmm) REVERT: B 310 ILE cc_start: 0.8770 (tt) cc_final: 0.8058 (mm) REVERT: B 313 ARG cc_start: 0.8864 (tpt-90) cc_final: 0.8210 (tpp-160) REVERT: B 314 MET cc_start: 0.8384 (tpt) cc_final: 0.7794 (mmm) REVERT: B 315 GLN cc_start: 0.8017 (mm110) cc_final: 0.7804 (mm110) REVERT: B 316 LYS cc_start: 0.8973 (ptpt) cc_final: 0.8599 (ptpt) REVERT: B 318 ILE cc_start: 0.8134 (mt) cc_final: 0.7923 (mm) REVERT: B 326 MET cc_start: 0.7329 (mmp) cc_final: 0.7076 (mmm) REVERT: B 329 LYS cc_start: 0.7329 (tmtt) cc_final: 0.6856 (tmtt) REVERT: B 335 GLU cc_start: 0.7984 (mp0) cc_final: 0.7779 (mm-30) REVERT: B 336 ARG cc_start: 0.7672 (mpt180) cc_final: 0.7431 (mpt180) REVERT: B 338 TYR cc_start: 0.7909 (m-80) cc_final: 0.7242 (m-80) REVERT: B 345 SER cc_start: 0.7363 (t) cc_final: 0.6951 (p) REVERT: B 351 SER cc_start: 0.8227 (t) cc_final: 0.7559 (p) REVERT: B 353 PHE cc_start: 0.8582 (t80) cc_final: 0.7927 (t80) REVERT: B 354 GLN cc_start: 0.8467 (mm110) cc_final: 0.8149 (mp10) REVERT: B 355 GLN cc_start: 0.8774 (pp30) cc_final: 0.7804 (pp30) REVERT: B 356 MET cc_start: 0.8477 (mtt) cc_final: 0.8213 (mmm) REVERT: B 365 GLU cc_start: 0.8284 (pt0) cc_final: 0.7994 (pp20) REVERT: B 372 HIS cc_start: 0.7838 (m-70) cc_final: 0.7166 (m-70) REVERT: C 50 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8543 (mtmt) REVERT: C 51 ASP cc_start: 0.8602 (p0) cc_final: 0.8134 (p0) REVERT: C 57 GLU cc_start: 0.8387 (pt0) cc_final: 0.8067 (pt0) REVERT: C 61 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8333 (mmtm) REVERT: C 64 ILE cc_start: 0.8383 (mt) cc_final: 0.7831 (tp) REVERT: C 76 ILE cc_start: 0.7459 (mm) cc_final: 0.7134 (tp) REVERT: C 82 MET cc_start: 0.7900 (tpp) cc_final: 0.6849 (tpp) REVERT: C 83 GLU cc_start: 0.8897 (pp20) cc_final: 0.8569 (pp20) REVERT: C 84 LYS cc_start: 0.9123 (ttmm) cc_final: 0.8719 (ttmm) REVERT: C 87 HIS cc_start: 0.8250 (t70) cc_final: 0.7526 (t-90) REVERT: C 90 PHE cc_start: 0.7803 (m-10) cc_final: 0.7314 (m-80) REVERT: C 91 TYR cc_start: 0.8014 (m-80) cc_final: 0.7507 (m-80) REVERT: C 105 LEU cc_start: 0.7934 (mm) cc_final: 0.7681 (mm) REVERT: C 111 ASN cc_start: 0.8849 (t0) cc_final: 0.8220 (t0) REVERT: C 113 LYS cc_start: 0.8429 (mttp) cc_final: 0.7993 (mttp) REVERT: C 117 GLU cc_start: 0.8409 (pp20) cc_final: 0.8168 (pp20) REVERT: C 119 MET cc_start: 0.8365 (ttm) cc_final: 0.8022 (ttm) REVERT: C 121 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8631 (tm-30) REVERT: C 123 MET cc_start: 0.8090 (tpp) cc_final: 0.7198 (tpp) REVERT: C 142 LEU cc_start: 0.8538 (tp) cc_final: 0.8299 (tp) REVERT: C 151 ILE cc_start: 0.8167 (tt) cc_final: 0.7578 (tp) REVERT: C 157 ASP cc_start: 0.7124 (t0) cc_final: 0.6476 (t0) REVERT: C 183 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: C 192 ILE cc_start: 0.8515 (mm) cc_final: 0.7861 (pt) REVERT: C 196 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7343 (ttm170) REVERT: C 205 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 211 ASP cc_start: 0.8853 (m-30) cc_final: 0.7744 (m-30) REVERT: C 212 ILE cc_start: 0.8839 (mt) cc_final: 0.8476 (mm) REVERT: C 240 TYR cc_start: 0.7958 (t80) cc_final: 0.7552 (t80) REVERT: C 252 ASN cc_start: 0.8168 (p0) cc_final: 0.7621 (p0) REVERT: C 253 GLU cc_start: 0.8164 (mp0) cc_final: 0.7685 (mp0) REVERT: C 256 ARG cc_start: 0.8549 (mtp180) cc_final: 0.7935 (mtp180) REVERT: C 259 GLU cc_start: 0.8792 (tp30) cc_final: 0.8100 (tp30) REVERT: C 262 PHE cc_start: 0.8772 (m-10) cc_final: 0.8399 (m-10) REVERT: C 263 GLN cc_start: 0.8017 (mt0) cc_final: 0.7732 (mt0) REVERT: C 276 GLU cc_start: 0.8503 (tp30) cc_final: 0.7681 (tp30) REVERT: C 280 ASN cc_start: 0.8685 (m110) cc_final: 0.7908 (m-40) REVERT: C 282 ILE cc_start: 0.8723 (mt) cc_final: 0.8394 (mt) REVERT: C 283 MET cc_start: 0.8319 (mmm) cc_final: 0.7876 (mmm) REVERT: C 284 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8421 (mtpt) REVERT: C 286 ASP cc_start: 0.8546 (t0) cc_final: 0.7932 (t70) REVERT: C 291 LYS cc_start: 0.7253 (mptt) cc_final: 0.7005 (mmtt) REVERT: C 294 TYR cc_start: 0.7950 (m-80) cc_final: 0.7586 (m-80) REVERT: C 296 ASN cc_start: 0.7337 (p0) cc_final: 0.6759 (p0) REVERT: C 299 MET cc_start: 0.7949 (mmm) cc_final: 0.7607 (mmm) REVERT: C 313 MET cc_start: 0.8234 (tpp) cc_final: 0.7193 (tpp) REVERT: C 314 GLN cc_start: 0.8523 (tt0) cc_final: 0.8264 (mt0) REVERT: C 316 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 317 ILE cc_start: 0.8781 (mm) cc_final: 0.8086 (mm) REVERT: C 326 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8559 (mmtt) REVERT: C 328 LYS cc_start: 0.8475 (mttp) cc_final: 0.8232 (mttp) REVERT: C 334 GLU cc_start: 0.8855 (pm20) cc_final: 0.8525 (pm20) REVERT: C 361 GLU cc_start: 0.8655 (tp30) cc_final: 0.8130 (tp30) REVERT: D 12 ASN cc_start: 0.7298 (m110) cc_final: 0.7091 (m-40) REVERT: D 24 ASP cc_start: 0.6482 (t0) cc_final: 0.5639 (m-30) REVERT: D 37 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7397 (tpp80) REVERT: D 41 GLN cc_start: 0.8098 (tp40) cc_final: 0.7582 (tm-30) REVERT: D 50 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7540 (mtmm) REVERT: D 52 SER cc_start: 0.7865 (t) cc_final: 0.7097 (m) REVERT: D 57 GLU cc_start: 0.8189 (tt0) cc_final: 0.7822 (tp30) REVERT: D 61 LYS cc_start: 0.8008 (mttt) cc_final: 0.7189 (mttt) REVERT: D 62 ARG cc_start: 0.8226 (mtm180) cc_final: 0.6178 (mtm-85) REVERT: D 81 ASP cc_start: 0.8202 (m-30) cc_final: 0.7382 (m-30) REVERT: D 84 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8609 (mtmt) REVERT: D 87 HIS cc_start: 0.8564 (t-90) cc_final: 0.8035 (t-90) REVERT: D 91 TYR cc_start: 0.8328 (m-80) cc_final: 0.7803 (m-80) REVERT: D 94 LEU cc_start: 0.8149 (mt) cc_final: 0.7934 (mt) REVERT: D 105 LEU cc_start: 0.7757 (mm) cc_final: 0.7109 (mm) REVERT: D 111 ASN cc_start: 0.8392 (m-40) cc_final: 0.7927 (m-40) REVERT: D 117 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7959 (mt-10) REVERT: D 119 MET cc_start: 0.8903 (ttm) cc_final: 0.8537 (ttm) REVERT: D 121 GLN cc_start: 0.8815 (pp30) cc_final: 0.8542 (pp30) REVERT: D 124 PHE cc_start: 0.7955 (m-80) cc_final: 0.7229 (m-80) REVERT: D 139 VAL cc_start: 0.8503 (m) cc_final: 0.8116 (p) REVERT: D 147 ARG cc_start: 0.7315 (mmt90) cc_final: 0.7064 (ttm110) REVERT: D 165 ILE cc_start: 0.7927 (mt) cc_final: 0.7613 (tt) REVERT: D 167 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7704 (mt-10) REVERT: D 176 MET cc_start: 0.7005 (mmm) cc_final: 0.6741 (mmm) REVERT: D 187 ASP cc_start: 0.8795 (m-30) cc_final: 0.8467 (m-30) REVERT: D 196 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7670 (tpp80) REVERT: D 205 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8386 (mt-10) REVERT: D 207 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7543 (tm-30) REVERT: D 210 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7604 (ttp80) REVERT: D 211 ASP cc_start: 0.8499 (m-30) cc_final: 0.7510 (m-30) REVERT: D 213 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8535 (ttpt) REVERT: D 214 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 240 TYR cc_start: 0.7916 (t80) cc_final: 0.7451 (t80) REVERT: D 243 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.7375 (Cg_endo) REVERT: D 259 GLU cc_start: 0.8423 (tp30) cc_final: 0.8019 (tp30) REVERT: D 279 TYR cc_start: 0.7971 (t80) cc_final: 0.7395 (t80) REVERT: D 283 MET cc_start: 0.8511 (mmp) cc_final: 0.8293 (mmp) REVERT: D 286 ASP cc_start: 0.8364 (t0) cc_final: 0.7896 (t0) REVERT: D 288 ASP cc_start: 0.8540 (m-30) cc_final: 0.7818 (m-30) REVERT: D 290 ARG cc_start: 0.7975 (mtt180) cc_final: 0.6966 (mtt180) REVERT: D 294 TYR cc_start: 0.8307 (m-80) cc_final: 0.7725 (m-80) REVERT: D 297 ASN cc_start: 0.7829 (m-40) cc_final: 0.7552 (m-40) REVERT: D 299 MET cc_start: 0.8140 (mmm) cc_final: 0.7889 (mmm) REVERT: D 305 MET cc_start: 0.7201 (mmp) cc_final: 0.6728 (mmt) REVERT: D 312 ARG cc_start: 0.8965 (tpt-90) cc_final: 0.8267 (tpt-90) REVERT: D 313 MET cc_start: 0.8471 (tpp) cc_final: 0.7476 (tpp) REVERT: D 314 GLN cc_start: 0.9042 (tt0) cc_final: 0.8681 (mm-40) REVERT: D 316 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8222 (mt-10) REVERT: D 320 LEU cc_start: 0.8844 (mt) cc_final: 0.8413 (mt) REVERT: D 334 GLU cc_start: 0.8318 (mp0) cc_final: 0.8039 (pm20) outliers start: 0 outliers final: 0 residues processed: 753 average time/residue: 0.3416 time to fit residues: 360.7704 Evaluate side-chains 688 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN B 74 HIS ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 40 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.111834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086197 restraints weight = 42641.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089883 restraints weight = 25337.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092464 restraints weight = 17093.151| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15177 Z= 0.213 Angle : 0.664 9.146 20547 Z= 0.338 Chirality : 0.044 0.190 2251 Planarity : 0.005 0.092 2631 Dihedral : 9.100 167.844 2071 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1847 helix: 1.06 (0.18), residues: 836 sheet: -1.19 (0.28), residues: 307 loop : 0.01 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 80 HIS 0.005 0.001 HIS C 275 PHE 0.024 0.001 PHE C 124 TYR 0.040 0.002 TYR A 477 ARG 0.015 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 760 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7329 (mm-30) REVERT: A 79 TYR cc_start: 0.7740 (m-80) cc_final: 0.7406 (m-80) REVERT: A 99 ILE cc_start: 0.8045 (pt) cc_final: 0.7600 (pt) REVERT: A 107 LEU cc_start: 0.7519 (tp) cc_final: 0.7300 (tp) REVERT: A 110 ILE cc_start: 0.7473 (mp) cc_final: 0.6996 (tp) REVERT: A 119 TYR cc_start: 0.7032 (m-80) cc_final: 0.6650 (m-80) REVERT: A 121 GLU cc_start: 0.8604 (pm20) cc_final: 0.8392 (tp30) REVERT: A 130 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8382 (mm110) REVERT: A 138 HIS cc_start: 0.6297 (t-170) cc_final: 0.5163 (t-90) REVERT: A 149 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8338 (mm-40) REVERT: A 156 ASN cc_start: 0.7285 (p0) cc_final: 0.6691 (t0) REVERT: A 174 LYS cc_start: 0.8861 (pttp) cc_final: 0.8515 (ptpp) REVERT: A 179 TYR cc_start: 0.8500 (t80) cc_final: 0.8151 (t80) REVERT: A 180 PHE cc_start: 0.8637 (m-80) cc_final: 0.8303 (m-80) REVERT: A 220 PHE cc_start: 0.7724 (p90) cc_final: 0.7169 (p90) REVERT: A 239 MET cc_start: 0.6996 (mmp) cc_final: 0.6444 (mmp) REVERT: A 242 TYR cc_start: 0.7259 (m-80) cc_final: 0.6886 (m-80) REVERT: A 248 ARG cc_start: 0.8490 (tpp80) cc_final: 0.7768 (tpp-160) REVERT: A 260 HIS cc_start: 0.8188 (m-70) cc_final: 0.7894 (m-70) REVERT: A 262 PHE cc_start: 0.8643 (m-80) cc_final: 0.8035 (m-80) REVERT: A 286 HIS cc_start: 0.6834 (t70) cc_final: 0.6495 (t-90) REVERT: A 307 HIS cc_start: 0.8849 (m90) cc_final: 0.8592 (m90) REVERT: A 309 ARG cc_start: 0.8858 (ppt170) cc_final: 0.8614 (ppt170) REVERT: A 312 CYS cc_start: 0.8631 (m) cc_final: 0.8117 (m) REVERT: A 317 ILE cc_start: 0.8586 (mt) cc_final: 0.7947 (mt) REVERT: A 322 GLN cc_start: 0.8788 (mt0) cc_final: 0.8524 (mp10) REVERT: A 327 ARG cc_start: 0.8583 (mpt180) cc_final: 0.8196 (mmt180) REVERT: A 354 HIS cc_start: 0.7676 (t-90) cc_final: 0.7246 (t70) REVERT: A 358 THR cc_start: 0.8347 (p) cc_final: 0.8068 (p) REVERT: A 364 MET cc_start: 0.7764 (mtt) cc_final: 0.7529 (mtt) REVERT: A 370 GLU cc_start: 0.8350 (tt0) cc_final: 0.7963 (tm-30) REVERT: A 371 MET cc_start: 0.9081 (mtm) cc_final: 0.8409 (ptm) REVERT: A 373 HIS cc_start: 0.8482 (t70) cc_final: 0.8100 (t70) REVERT: A 423 LEU cc_start: 0.7472 (mt) cc_final: 0.6935 (mt) REVERT: A 451 GLN cc_start: 0.8794 (mp10) cc_final: 0.8145 (mp10) REVERT: A 452 PHE cc_start: 0.8524 (t80) cc_final: 0.7946 (t80) REVERT: A 463 GLN cc_start: 0.8920 (tt0) cc_final: 0.8222 (mm-40) REVERT: A 466 ASN cc_start: 0.7997 (m-40) cc_final: 0.7459 (m-40) REVERT: A 468 HIS cc_start: 0.8274 (t-90) cc_final: 0.7709 (t-90) REVERT: A 470 PHE cc_start: 0.8200 (m-80) cc_final: 0.7643 (m-80) REVERT: A 475 GLU cc_start: 0.8492 (pp20) cc_final: 0.8255 (pp20) REVERT: A 478 MET cc_start: 0.8802 (mtm) cc_final: 0.8425 (mtm) REVERT: A 493 GLN cc_start: 0.8727 (tp-100) cc_final: 0.7979 (tp40) REVERT: A 498 LEU cc_start: 0.9046 (mp) cc_final: 0.8420 (tt) REVERT: A 511 GLU cc_start: 0.8601 (tp30) cc_final: 0.7430 (tp30) REVERT: A 512 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 515 MET cc_start: 0.7217 (ttm) cc_final: 0.6670 (tpt) REVERT: A 520 ASP cc_start: 0.8445 (p0) cc_final: 0.8196 (m-30) REVERT: A 525 GLN cc_start: 0.8500 (tp40) cc_final: 0.7446 (tp-100) REVERT: A 526 LYS cc_start: 0.9027 (tttt) cc_final: 0.8265 (tppt) REVERT: A 529 ASN cc_start: 0.8556 (m-40) cc_final: 0.7575 (m-40) REVERT: A 532 LEU cc_start: 0.7917 (mt) cc_final: 0.7230 (mt) REVERT: A 537 LEU cc_start: 0.9047 (mp) cc_final: 0.8755 (mp) REVERT: A 538 PHE cc_start: 0.8111 (t80) cc_final: 0.7416 (t80) REVERT: A 545 ASN cc_start: 0.8249 (t0) cc_final: 0.8020 (t0) REVERT: A 556 LYS cc_start: 0.8632 (mttt) cc_final: 0.8087 (mtpp) REVERT: A 558 GLU cc_start: 0.7827 (tt0) cc_final: 0.7450 (tm-30) REVERT: A 559 TYR cc_start: 0.7380 (m-80) cc_final: 0.6847 (m-80) REVERT: A 568 ASN cc_start: 0.8328 (t0) cc_final: 0.7948 (t0) REVERT: A 574 GLU cc_start: 0.8666 (tp30) cc_final: 0.8208 (pm20) REVERT: A 633 LYS cc_start: 0.7307 (mtmm) cc_final: 0.6596 (mmtm) REVERT: A 637 HIS cc_start: 0.8125 (t-90) cc_final: 0.7583 (t-90) REVERT: A 638 GLN cc_start: 0.8889 (tt0) cc_final: 0.8653 (pt0) REVERT: A 640 ARG cc_start: 0.8959 (ptp-170) cc_final: 0.8684 (ptm-80) REVERT: A 641 ASN cc_start: 0.9019 (m110) cc_final: 0.8565 (m-40) REVERT: A 643 LEU cc_start: 0.8667 (tp) cc_final: 0.7563 (tp) REVERT: A 647 MET cc_start: 0.8695 (mmm) cc_final: 0.7938 (mmm) REVERT: A 648 GLU cc_start: 0.8736 (tp30) cc_final: 0.8316 (tm-30) REVERT: A 649 THR cc_start: 0.9044 (p) cc_final: 0.8643 (p) REVERT: A 650 LEU cc_start: 0.8748 (mm) cc_final: 0.8406 (pp) REVERT: A 651 ASN cc_start: 0.8698 (m110) cc_final: 0.8447 (m110) REVERT: A 657 TYR cc_start: 0.6668 (m-80) cc_final: 0.6138 (m-80) REVERT: A 666 PHE cc_start: 0.8363 (m-10) cc_final: 0.8016 (m-10) REVERT: A 741 TYR cc_start: 0.8495 (p90) cc_final: 0.8247 (p90) REVERT: A 750 PHE cc_start: 0.8997 (m-10) cc_final: 0.8737 (m-10) REVERT: A 757 TYR cc_start: 0.8955 (t80) cc_final: 0.8586 (t80) REVERT: B 35 ILE cc_start: 0.8501 (mt) cc_final: 0.7971 (tp) REVERT: B 48 MET cc_start: 0.7205 (mmt) cc_final: 0.6606 (tpp) REVERT: B 51 LYS cc_start: 0.8793 (mppt) cc_final: 0.8515 (mmtm) REVERT: B 54 TYR cc_start: 0.7914 (m-10) cc_final: 0.7667 (m-10) REVERT: B 58 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8016 (tt0) REVERT: B 83 MET cc_start: 0.8250 (tpp) cc_final: 0.7693 (tpp) REVERT: B 84 GLU cc_start: 0.8794 (tt0) cc_final: 0.8366 (tm-30) REVERT: B 85 LYS cc_start: 0.9213 (mttm) cc_final: 0.8887 (mttm) REVERT: B 93 ASN cc_start: 0.8183 (m110) cc_final: 0.7868 (m110) REVERT: B 106 LEU cc_start: 0.7960 (mt) cc_final: 0.7751 (mt) REVERT: B 108 GLU cc_start: 0.6690 (pp20) cc_final: 0.6470 (pp20) REVERT: B 111 LEU cc_start: 0.8486 (mt) cc_final: 0.7746 (mt) REVERT: B 114 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8068 (ptmm) REVERT: B 118 GLU cc_start: 0.8182 (mt-10) cc_final: 0.6908 (mm-30) REVERT: B 120 MET cc_start: 0.8429 (ttm) cc_final: 0.7852 (tmm) REVERT: B 121 THR cc_start: 0.8648 (p) cc_final: 0.7899 (p) REVERT: B 124 MET cc_start: 0.8246 (tpp) cc_final: 0.7531 (tpp) REVERT: B 128 PHE cc_start: 0.8114 (m-80) cc_final: 0.7124 (m-80) REVERT: B 133 MET cc_start: 0.7404 (ttp) cc_final: 0.6848 (ttp) REVERT: B 134 TYR cc_start: 0.7279 (t80) cc_final: 0.7019 (t80) REVERT: B 155 ASP cc_start: 0.6774 (t0) cc_final: 0.6348 (t0) REVERT: B 168 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7681 (mm-30) REVERT: B 176 ILE cc_start: 0.8204 (mt) cc_final: 0.8000 (tp) REVERT: B 178 ARG cc_start: 0.7013 (ttm170) cc_final: 0.6791 (ttm-80) REVERT: B 179 LEU cc_start: 0.6975 (tp) cc_final: 0.6535 (tp) REVERT: B 186 LEU cc_start: 0.8686 (mt) cc_final: 0.8484 (mt) REVERT: B 192 LYS cc_start: 0.8343 (ptmt) cc_final: 0.8022 (ptmt) REVERT: B 193 ILE cc_start: 0.8846 (pt) cc_final: 0.8270 (tt) REVERT: B 207 ARG cc_start: 0.8738 (ttm170) cc_final: 0.8080 (ttm-80) REVERT: B 208 GLU cc_start: 0.8779 (tp30) cc_final: 0.8158 (tm-30) REVERT: B 209 ILE cc_start: 0.8923 (mm) cc_final: 0.8692 (mm) REVERT: B 212 ASP cc_start: 0.8992 (m-30) cc_final: 0.7750 (m-30) REVERT: B 214 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8553 (ttpt) REVERT: B 216 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8570 (mmmm) REVERT: B 219 TYR cc_start: 0.7597 (p90) cc_final: 0.7293 (p90) REVERT: B 226 ASN cc_start: 0.8539 (t0) cc_final: 0.8068 (t0) REVERT: B 230 THR cc_start: 0.8436 (m) cc_final: 0.8089 (p) REVERT: B 239 LYS cc_start: 0.8566 (mttt) cc_final: 0.8279 (mmtt) REVERT: B 256 PHE cc_start: 0.8429 (p90) cc_final: 0.8188 (p90) REVERT: B 260 GLU cc_start: 0.8473 (tp30) cc_final: 0.8136 (tp30) REVERT: B 263 PHE cc_start: 0.8615 (m-80) cc_final: 0.7798 (m-80) REVERT: B 264 GLN cc_start: 0.8590 (tp-100) cc_final: 0.7308 (mt0) REVERT: B 267 PHE cc_start: 0.8283 (m-10) cc_final: 0.7604 (m-10) REVERT: B 277 GLU cc_start: 0.8495 (tp30) cc_final: 0.8185 (tp30) REVERT: B 292 LYS cc_start: 0.8685 (pttm) cc_final: 0.8299 (pttm) REVERT: B 293 ASP cc_start: 0.8761 (m-30) cc_final: 0.8516 (m-30) REVERT: B 298 ASN cc_start: 0.7122 (m-40) cc_final: 0.6428 (m-40) REVERT: B 300 MET cc_start: 0.7884 (mmm) cc_final: 0.7607 (mmm) REVERT: B 310 ILE cc_start: 0.8814 (tt) cc_final: 0.8119 (mm) REVERT: B 313 ARG cc_start: 0.8852 (tpt-90) cc_final: 0.8230 (tpp-160) REVERT: B 314 MET cc_start: 0.8398 (tpt) cc_final: 0.7810 (mmm) REVERT: B 315 GLN cc_start: 0.8009 (mm110) cc_final: 0.7577 (tp40) REVERT: B 316 LYS cc_start: 0.8933 (ptpt) cc_final: 0.8610 (ptpt) REVERT: B 318 ILE cc_start: 0.8182 (mt) cc_final: 0.7933 (mm) REVERT: B 326 MET cc_start: 0.7344 (mmp) cc_final: 0.7040 (mmm) REVERT: B 329 LYS cc_start: 0.7380 (tmtt) cc_final: 0.6875 (tmtt) REVERT: B 338 TYR cc_start: 0.8086 (m-80) cc_final: 0.7424 (m-80) REVERT: B 351 SER cc_start: 0.8393 (t) cc_final: 0.7619 (p) REVERT: B 353 PHE cc_start: 0.8449 (t80) cc_final: 0.8031 (t80) REVERT: B 355 GLN cc_start: 0.8761 (pp30) cc_final: 0.7956 (pp30) REVERT: B 356 MET cc_start: 0.8425 (mtt) cc_final: 0.8058 (mmm) REVERT: B 360 LYS cc_start: 0.8199 (tptp) cc_final: 0.7466 (tptp) REVERT: B 361 GLN cc_start: 0.8597 (pp30) cc_final: 0.8289 (pp30) REVERT: B 372 HIS cc_start: 0.7996 (m-70) cc_final: 0.7417 (m90) REVERT: C 50 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8468 (mtmt) REVERT: C 51 ASP cc_start: 0.8564 (p0) cc_final: 0.8200 (p0) REVERT: C 54 VAL cc_start: 0.7824 (t) cc_final: 0.7370 (p) REVERT: C 61 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8081 (mmtm) REVERT: C 64 ILE cc_start: 0.8419 (mt) cc_final: 0.7840 (tp) REVERT: C 75 ILE cc_start: 0.8088 (pt) cc_final: 0.7590 (pt) REVERT: C 76 ILE cc_start: 0.7498 (mm) cc_final: 0.6868 (tp) REVERT: C 82 MET cc_start: 0.7941 (tpp) cc_final: 0.7026 (tpp) REVERT: C 83 GLU cc_start: 0.8868 (pp20) cc_final: 0.8592 (pp20) REVERT: C 84 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8822 (ttmm) REVERT: C 87 HIS cc_start: 0.8213 (t70) cc_final: 0.7503 (t-90) REVERT: C 90 PHE cc_start: 0.7844 (m-10) cc_final: 0.7279 (m-80) REVERT: C 91 TYR cc_start: 0.8015 (m-80) cc_final: 0.7490 (m-80) REVERT: C 105 LEU cc_start: 0.8126 (mm) cc_final: 0.7910 (mm) REVERT: C 111 ASN cc_start: 0.8947 (t0) cc_final: 0.8399 (t0) REVERT: C 117 GLU cc_start: 0.8431 (pp20) cc_final: 0.8156 (pp20) REVERT: C 119 MET cc_start: 0.8321 (ttm) cc_final: 0.8010 (ttm) REVERT: C 121 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 123 MET cc_start: 0.8235 (tpp) cc_final: 0.7340 (tpp) REVERT: C 127 PHE cc_start: 0.8055 (m-80) cc_final: 0.7363 (m-80) REVERT: C 140 LEU cc_start: 0.8891 (mt) cc_final: 0.8689 (mt) REVERT: C 151 ILE cc_start: 0.8197 (tt) cc_final: 0.7419 (tp) REVERT: C 153 LEU cc_start: 0.8389 (tp) cc_final: 0.8090 (tp) REVERT: C 157 ASP cc_start: 0.7165 (t0) cc_final: 0.6515 (t0) REVERT: C 164 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7346 (Cg_exo) REVERT: C 166 TYR cc_start: 0.8016 (t80) cc_final: 0.7163 (t80) REVERT: C 167 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 183 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.8077 (ttm-80) REVERT: C 187 ASP cc_start: 0.8837 (m-30) cc_final: 0.8573 (m-30) REVERT: C 192 ILE cc_start: 0.8632 (mm) cc_final: 0.7990 (pt) REVERT: C 205 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 207 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 210 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8327 (ttp80) REVERT: C 211 ASP cc_start: 0.8186 (m-30) cc_final: 0.7759 (m-30) REVERT: C 212 ILE cc_start: 0.8837 (mt) cc_final: 0.8514 (mm) REVERT: C 240 TYR cc_start: 0.7860 (t80) cc_final: 0.7432 (t80) REVERT: C 242 LEU cc_start: 0.8804 (mt) cc_final: 0.8245 (mt) REVERT: C 252 ASN cc_start: 0.8206 (p0) cc_final: 0.7657 (p0) REVERT: C 253 GLU cc_start: 0.8226 (mp0) cc_final: 0.7719 (mp0) REVERT: C 256 ARG cc_start: 0.8572 (mtp180) cc_final: 0.7962 (mtp180) REVERT: C 259 GLU cc_start: 0.8827 (tp30) cc_final: 0.8151 (tp30) REVERT: C 262 PHE cc_start: 0.8742 (m-10) cc_final: 0.8374 (m-10) REVERT: C 263 GLN cc_start: 0.8039 (mt0) cc_final: 0.7750 (mt0) REVERT: C 276 GLU cc_start: 0.8539 (tp30) cc_final: 0.7739 (tp30) REVERT: C 280 ASN cc_start: 0.8702 (m110) cc_final: 0.7928 (m-40) REVERT: C 282 ILE cc_start: 0.8736 (mt) cc_final: 0.8412 (mt) REVERT: C 283 MET cc_start: 0.8342 (mmm) cc_final: 0.7934 (mmm) REVERT: C 284 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8397 (mtpt) REVERT: C 289 ILE cc_start: 0.8215 (mp) cc_final: 0.7668 (mm) REVERT: C 290 ARG cc_start: 0.7845 (mtt180) cc_final: 0.6910 (mtt90) REVERT: C 294 TYR cc_start: 0.7976 (m-80) cc_final: 0.7652 (m-80) REVERT: C 296 ASN cc_start: 0.7256 (p0) cc_final: 0.6644 (p0) REVERT: C 299 MET cc_start: 0.7853 (mmm) cc_final: 0.7572 (mmm) REVERT: C 305 MET cc_start: 0.6837 (mmm) cc_final: 0.6412 (mmm) REVERT: C 313 MET cc_start: 0.8216 (tpp) cc_final: 0.7191 (tpp) REVERT: C 314 GLN cc_start: 0.8560 (tt0) cc_final: 0.8313 (mt0) REVERT: C 316 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 317 ILE cc_start: 0.8825 (mm) cc_final: 0.8229 (mm) REVERT: C 325 MET cc_start: 0.7720 (tpt) cc_final: 0.7433 (tpt) REVERT: C 328 LYS cc_start: 0.8498 (mttp) cc_final: 0.8245 (mttp) REVERT: C 334 GLU cc_start: 0.8952 (pm20) cc_final: 0.8629 (pm20) REVERT: C 361 GLU cc_start: 0.8682 (tp30) cc_final: 0.8310 (tm-30) REVERT: D 24 ASP cc_start: 0.6540 (t0) cc_final: 0.6189 (t0) REVERT: D 33 SER cc_start: 0.8165 (p) cc_final: 0.7909 (p) REVERT: D 37 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7482 (tpp80) REVERT: D 41 GLN cc_start: 0.8049 (tp40) cc_final: 0.7717 (tm-30) REVERT: D 52 SER cc_start: 0.7821 (t) cc_final: 0.7198 (m) REVERT: D 62 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7860 (mtm-85) REVERT: D 65 LEU cc_start: 0.8401 (mt) cc_final: 0.8113 (mt) REVERT: D 67 LEU cc_start: 0.8033 (mt) cc_final: 0.7816 (mt) REVERT: D 81 ASP cc_start: 0.8177 (m-30) cc_final: 0.7394 (m-30) REVERT: D 84 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8563 (mtmt) REVERT: D 87 HIS cc_start: 0.8558 (t-90) cc_final: 0.7972 (t-90) REVERT: D 91 TYR cc_start: 0.8470 (m-80) cc_final: 0.7775 (m-80) REVERT: D 92 ASN cc_start: 0.7875 (m110) cc_final: 0.7674 (m110) REVERT: D 99 GLU cc_start: 0.7612 (mp0) cc_final: 0.7332 (mp0) REVERT: D 116 ARG cc_start: 0.8597 (tpp-160) cc_final: 0.8222 (tpp-160) REVERT: D 119 MET cc_start: 0.8855 (ttm) cc_final: 0.8575 (ttm) REVERT: D 121 GLN cc_start: 0.8884 (pp30) cc_final: 0.8632 (pp30) REVERT: D 124 PHE cc_start: 0.7954 (m-80) cc_final: 0.7323 (m-80) REVERT: D 139 VAL cc_start: 0.8520 (m) cc_final: 0.8134 (p) REVERT: D 147 ARG cc_start: 0.7313 (mmt90) cc_final: 0.7103 (ttm110) REVERT: D 165 ILE cc_start: 0.7941 (mt) cc_final: 0.7623 (tt) REVERT: D 176 MET cc_start: 0.7080 (mmm) cc_final: 0.6839 (mmm) REVERT: D 187 ASP cc_start: 0.8750 (m-30) cc_final: 0.8435 (m-30) REVERT: D 191 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8832 (ttpt) REVERT: D 196 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7596 (tpp80) REVERT: D 207 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7440 (mm-30) REVERT: D 210 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7789 (ttp80) REVERT: D 211 ASP cc_start: 0.8464 (m-30) cc_final: 0.8166 (m-30) REVERT: D 213 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8507 (ttpt) REVERT: D 214 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 215 LYS cc_start: 0.9015 (mmpt) cc_final: 0.8778 (mmmt) REVERT: D 225 ASN cc_start: 0.8655 (m-40) cc_final: 0.8393 (m110) REVERT: D 240 TYR cc_start: 0.7924 (t80) cc_final: 0.7465 (t80) REVERT: D 243 PRO cc_start: 0.8340 (Cg_exo) cc_final: 0.7448 (Cg_endo) REVERT: D 259 GLU cc_start: 0.8385 (tp30) cc_final: 0.8018 (tp30) REVERT: D 267 ILE cc_start: 0.8843 (mt) cc_final: 0.8391 (tp) REVERT: D 269 MET cc_start: 0.8256 (mmp) cc_final: 0.7993 (mmp) REVERT: D 276 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8237 (mt-10) REVERT: D 279 TYR cc_start: 0.8055 (t80) cc_final: 0.7520 (t80) REVERT: D 283 MET cc_start: 0.8568 (mmp) cc_final: 0.8367 (mmp) REVERT: D 286 ASP cc_start: 0.8386 (t0) cc_final: 0.7855 (t0) REVERT: D 287 ILE cc_start: 0.8503 (tp) cc_final: 0.8112 (tt) REVERT: D 288 ASP cc_start: 0.8474 (m-30) cc_final: 0.7798 (m-30) REVERT: D 289 ILE cc_start: 0.8177 (pt) cc_final: 0.7891 (pt) REVERT: D 290 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7040 (mtt90) REVERT: D 292 ASP cc_start: 0.8612 (m-30) cc_final: 0.7483 (t0) REVERT: D 293 LEU cc_start: 0.9020 (mt) cc_final: 0.8643 (mt) REVERT: D 294 TYR cc_start: 0.8395 (m-80) cc_final: 0.7728 (m-80) REVERT: D 297 ASN cc_start: 0.7850 (m-40) cc_final: 0.7563 (m-40) REVERT: D 299 MET cc_start: 0.8166 (mmm) cc_final: 0.7935 (mmm) REVERT: D 305 MET cc_start: 0.7142 (mmp) cc_final: 0.6868 (mmm) REVERT: D 312 ARG cc_start: 0.8950 (tpt-90) cc_final: 0.8244 (tpt-90) REVERT: D 313 MET cc_start: 0.8513 (tpp) cc_final: 0.7523 (tpp) REVERT: D 314 GLN cc_start: 0.9007 (tt0) cc_final: 0.8695 (mm-40) REVERT: D 316 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8220 (mt-10) REVERT: D 320 LEU cc_start: 0.8851 (mt) cc_final: 0.8440 (mt) REVERT: D 346 LEU cc_start: 0.8325 (tp) cc_final: 0.7980 (tp) REVERT: D 371 HIS cc_start: 0.7641 (p90) cc_final: 0.7220 (p90) outliers start: 0 outliers final: 0 residues processed: 760 average time/residue: 0.3206 time to fit residues: 337.4920 Evaluate side-chains 721 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 1 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 63 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 12 ASN C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086836 restraints weight = 42523.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090585 restraints weight = 25264.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093204 restraints weight = 17021.633| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15177 Z= 0.190 Angle : 0.667 13.379 20547 Z= 0.335 Chirality : 0.044 0.235 2251 Planarity : 0.005 0.078 2631 Dihedral : 8.994 168.655 2071 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1847 helix: 1.11 (0.18), residues: 835 sheet: -1.05 (0.29), residues: 303 loop : -0.09 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.009 0.001 HIS D 161 PHE 0.016 0.001 PHE C 124 TYR 0.036 0.001 TYR A 477 ARG 0.010 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 763 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7358 (mm-30) REVERT: A 79 TYR cc_start: 0.7869 (m-80) cc_final: 0.7515 (m-80) REVERT: A 99 ILE cc_start: 0.8036 (pt) cc_final: 0.7690 (pt) REVERT: A 110 ILE cc_start: 0.7547 (mp) cc_final: 0.7040 (tp) REVERT: A 121 GLU cc_start: 0.8560 (pm20) cc_final: 0.8356 (tp30) REVERT: A 125 ASN cc_start: 0.9091 (m110) cc_final: 0.8152 (m110) REVERT: A 130 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8334 (mm110) REVERT: A 132 MET cc_start: 0.6865 (ttm) cc_final: 0.6284 (ttm) REVERT: A 138 HIS cc_start: 0.5819 (t-170) cc_final: 0.5577 (t-90) REVERT: A 149 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8340 (mm-40) REVERT: A 156 ASN cc_start: 0.7251 (p0) cc_final: 0.6691 (t0) REVERT: A 174 LYS cc_start: 0.8864 (pttp) cc_final: 0.8527 (pttm) REVERT: A 179 TYR cc_start: 0.8432 (t80) cc_final: 0.8106 (t80) REVERT: A 180 PHE cc_start: 0.8647 (m-80) cc_final: 0.8303 (m-80) REVERT: A 220 PHE cc_start: 0.7618 (p90) cc_final: 0.7018 (p90) REVERT: A 223 TYR cc_start: 0.7877 (t80) cc_final: 0.7654 (t80) REVERT: A 239 MET cc_start: 0.6968 (mmp) cc_final: 0.6392 (mmp) REVERT: A 242 TYR cc_start: 0.7236 (m-80) cc_final: 0.6835 (m-80) REVERT: A 248 ARG cc_start: 0.8544 (tpp80) cc_final: 0.7969 (tpp-160) REVERT: A 260 HIS cc_start: 0.7937 (m-70) cc_final: 0.7675 (m-70) REVERT: A 262 PHE cc_start: 0.8630 (m-80) cc_final: 0.8043 (m-80) REVERT: A 286 HIS cc_start: 0.6923 (t70) cc_final: 0.6545 (t70) REVERT: A 304 GLU cc_start: 0.8052 (mp0) cc_final: 0.7657 (mp0) REVERT: A 307 HIS cc_start: 0.8871 (m90) cc_final: 0.8646 (m90) REVERT: A 309 ARG cc_start: 0.8851 (ppt170) cc_final: 0.8590 (ppt170) REVERT: A 312 CYS cc_start: 0.8630 (m) cc_final: 0.8115 (m) REVERT: A 317 ILE cc_start: 0.8607 (mt) cc_final: 0.7996 (mt) REVERT: A 322 GLN cc_start: 0.8787 (mt0) cc_final: 0.8542 (mp10) REVERT: A 327 ARG cc_start: 0.8594 (mpt180) cc_final: 0.8191 (mmt-90) REVERT: A 329 LEU cc_start: 0.8603 (mt) cc_final: 0.8191 (pp) REVERT: A 354 HIS cc_start: 0.7963 (t-90) cc_final: 0.7275 (t70) REVERT: A 358 THR cc_start: 0.8622 (p) cc_final: 0.8107 (p) REVERT: A 370 GLU cc_start: 0.8376 (tt0) cc_final: 0.7961 (tm-30) REVERT: A 371 MET cc_start: 0.9145 (mtm) cc_final: 0.8295 (mtp) REVERT: A 373 HIS cc_start: 0.8443 (t70) cc_final: 0.8046 (t70) REVERT: A 408 TYR cc_start: 0.8698 (t80) cc_final: 0.7932 (t80) REVERT: A 423 LEU cc_start: 0.7502 (mt) cc_final: 0.6932 (mt) REVERT: A 451 GLN cc_start: 0.8748 (mp10) cc_final: 0.8406 (mp10) REVERT: A 466 ASN cc_start: 0.8023 (m-40) cc_final: 0.7520 (m-40) REVERT: A 468 HIS cc_start: 0.8270 (t-90) cc_final: 0.7732 (t-90) REVERT: A 470 PHE cc_start: 0.8200 (m-80) cc_final: 0.7550 (m-80) REVERT: A 475 GLU cc_start: 0.8466 (pp20) cc_final: 0.8229 (pp20) REVERT: A 478 MET cc_start: 0.8776 (mtm) cc_final: 0.8389 (mtm) REVERT: A 498 LEU cc_start: 0.9044 (mp) cc_final: 0.8431 (tt) REVERT: A 511 GLU cc_start: 0.8457 (tp30) cc_final: 0.8097 (tp30) REVERT: A 515 MET cc_start: 0.7171 (ttm) cc_final: 0.6570 (tpt) REVERT: A 525 GLN cc_start: 0.8483 (tp40) cc_final: 0.7431 (tp-100) REVERT: A 526 LYS cc_start: 0.9056 (tttt) cc_final: 0.8253 (tppt) REVERT: A 529 ASN cc_start: 0.8534 (m-40) cc_final: 0.7552 (m110) REVERT: A 532 LEU cc_start: 0.7871 (mt) cc_final: 0.7164 (mt) REVERT: A 537 LEU cc_start: 0.9043 (mp) cc_final: 0.8768 (mp) REVERT: A 538 PHE cc_start: 0.8002 (t80) cc_final: 0.7206 (t80) REVERT: A 542 ARG cc_start: 0.8095 (tmm-80) cc_final: 0.7744 (tmm-80) REVERT: A 556 LYS cc_start: 0.8642 (mttt) cc_final: 0.8094 (mtpp) REVERT: A 558 GLU cc_start: 0.7786 (tt0) cc_final: 0.7411 (tm-30) REVERT: A 559 TYR cc_start: 0.7301 (m-80) cc_final: 0.6747 (m-80) REVERT: A 568 ASN cc_start: 0.8284 (t0) cc_final: 0.8019 (t0) REVERT: A 587 MET cc_start: 0.8618 (mmp) cc_final: 0.8174 (pmm) REVERT: A 633 LYS cc_start: 0.7358 (mtmm) cc_final: 0.6806 (mmtt) REVERT: A 637 HIS cc_start: 0.8098 (t-90) cc_final: 0.7590 (t-90) REVERT: A 638 GLN cc_start: 0.8850 (tt0) cc_final: 0.8607 (pt0) REVERT: A 641 ASN cc_start: 0.9022 (m110) cc_final: 0.8538 (m-40) REVERT: A 643 LEU cc_start: 0.8658 (tp) cc_final: 0.7236 (tp) REVERT: A 647 MET cc_start: 0.8644 (mmm) cc_final: 0.7817 (mmm) REVERT: A 650 LEU cc_start: 0.8761 (mm) cc_final: 0.8354 (pp) REVERT: A 657 TYR cc_start: 0.6679 (m-80) cc_final: 0.6176 (m-80) REVERT: A 666 PHE cc_start: 0.8341 (m-10) cc_final: 0.7816 (m-10) REVERT: A 676 ARG cc_start: 0.8591 (mmp80) cc_final: 0.7954 (mtt90) REVERT: A 682 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8457 (ptt-90) REVERT: A 701 TRP cc_start: 0.8281 (m100) cc_final: 0.8077 (m100) REVERT: A 750 PHE cc_start: 0.8978 (m-10) cc_final: 0.8570 (m-10) REVERT: A 757 TYR cc_start: 0.8944 (t80) cc_final: 0.8543 (t80) REVERT: B 32 PHE cc_start: 0.7798 (p90) cc_final: 0.7562 (p90) REVERT: B 35 ILE cc_start: 0.8524 (mt) cc_final: 0.7992 (tp) REVERT: B 38 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: B 51 LYS cc_start: 0.8822 (mppt) cc_final: 0.8606 (mmtm) REVERT: B 58 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7999 (tt0) REVERT: B 82 ASP cc_start: 0.8559 (m-30) cc_final: 0.8106 (m-30) REVERT: B 83 MET cc_start: 0.8235 (tpp) cc_final: 0.7746 (tpp) REVERT: B 84 GLU cc_start: 0.8787 (tt0) cc_final: 0.8322 (tm-30) REVERT: B 85 LYS cc_start: 0.9225 (mttm) cc_final: 0.8895 (mttm) REVERT: B 114 LYS cc_start: 0.8539 (ptmm) cc_final: 0.7978 (ptmm) REVERT: B 118 GLU cc_start: 0.8170 (mt-10) cc_final: 0.6929 (mm-30) REVERT: B 120 MET cc_start: 0.8484 (ttm) cc_final: 0.7849 (tmm) REVERT: B 121 THR cc_start: 0.8608 (p) cc_final: 0.7922 (p) REVERT: B 124 MET cc_start: 0.8388 (tpp) cc_final: 0.7549 (tpp) REVERT: B 128 PHE cc_start: 0.8078 (m-80) cc_final: 0.7134 (m-80) REVERT: B 133 MET cc_start: 0.7498 (ttp) cc_final: 0.6896 (ttp) REVERT: B 134 TYR cc_start: 0.7319 (t80) cc_final: 0.6917 (t80) REVERT: B 155 ASP cc_start: 0.6709 (t0) cc_final: 0.6300 (t0) REVERT: B 163 ASN cc_start: 0.8158 (t0) cc_final: 0.7914 (t0) REVERT: B 168 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 179 LEU cc_start: 0.7054 (tp) cc_final: 0.6660 (tp) REVERT: B 184 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7881 (ttm110) REVERT: B 186 LEU cc_start: 0.8738 (mt) cc_final: 0.8528 (mt) REVERT: B 192 LYS cc_start: 0.8316 (ptmt) cc_final: 0.8016 (ptmt) REVERT: B 193 ILE cc_start: 0.8848 (pt) cc_final: 0.8280 (tt) REVERT: B 207 ARG cc_start: 0.8713 (ttm170) cc_final: 0.8044 (ttm-80) REVERT: B 208 GLU cc_start: 0.8786 (tp30) cc_final: 0.8163 (tm-30) REVERT: B 209 ILE cc_start: 0.8854 (mm) cc_final: 0.8615 (mm) REVERT: B 212 ASP cc_start: 0.8989 (m-30) cc_final: 0.7714 (m-30) REVERT: B 214 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8530 (ttpt) REVERT: B 216 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8547 (mmmm) REVERT: B 219 TYR cc_start: 0.7516 (p90) cc_final: 0.7248 (p90) REVERT: B 226 ASN cc_start: 0.8566 (t0) cc_final: 0.8085 (t0) REVERT: B 230 THR cc_start: 0.8441 (m) cc_final: 0.8152 (p) REVERT: B 239 LYS cc_start: 0.8588 (mttt) cc_final: 0.8316 (mmtt) REVERT: B 256 PHE cc_start: 0.8480 (p90) cc_final: 0.8276 (p90) REVERT: B 263 PHE cc_start: 0.8641 (m-80) cc_final: 0.7821 (m-80) REVERT: B 264 GLN cc_start: 0.8602 (tp-100) cc_final: 0.7411 (mt0) REVERT: B 267 PHE cc_start: 0.8305 (m-10) cc_final: 0.7680 (m-10) REVERT: B 277 GLU cc_start: 0.8470 (tp30) cc_final: 0.8107 (tp30) REVERT: B 281 ASN cc_start: 0.8544 (t0) cc_final: 0.8308 (t0) REVERT: B 298 ASN cc_start: 0.7105 (m-40) cc_final: 0.6446 (m-40) REVERT: B 300 MET cc_start: 0.7887 (mmm) cc_final: 0.7644 (mmm) REVERT: B 306 MET cc_start: 0.7360 (mmt) cc_final: 0.7148 (mmt) REVERT: B 310 ILE cc_start: 0.8839 (tt) cc_final: 0.8198 (mm) REVERT: B 313 ARG cc_start: 0.8871 (tpt-90) cc_final: 0.8264 (tpp-160) REVERT: B 314 MET cc_start: 0.8419 (tpt) cc_final: 0.7827 (mmm) REVERT: B 315 GLN cc_start: 0.7904 (mm110) cc_final: 0.7509 (tp40) REVERT: B 316 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8612 (ptpt) REVERT: B 326 MET cc_start: 0.7307 (mmp) cc_final: 0.7060 (mmm) REVERT: B 329 LYS cc_start: 0.7395 (tmtt) cc_final: 0.6871 (tmtt) REVERT: B 335 GLU cc_start: 0.8151 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 336 ARG cc_start: 0.7705 (mpt180) cc_final: 0.7460 (mpt180) REVERT: B 338 TYR cc_start: 0.8033 (m-80) cc_final: 0.7266 (m-80) REVERT: B 351 SER cc_start: 0.8206 (t) cc_final: 0.7335 (t) REVERT: B 353 PHE cc_start: 0.8294 (t80) cc_final: 0.7998 (t80) REVERT: B 357 TRP cc_start: 0.5756 (m100) cc_final: 0.5123 (m100) REVERT: B 360 LYS cc_start: 0.8163 (tptp) cc_final: 0.7448 (tptp) REVERT: B 372 HIS cc_start: 0.8011 (m-70) cc_final: 0.7417 (m90) REVERT: C 44 MET cc_start: 0.8545 (ppp) cc_final: 0.7993 (ppp) REVERT: C 50 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8491 (mtmt) REVERT: C 51 ASP cc_start: 0.8556 (p0) cc_final: 0.8116 (p0) REVERT: C 54 VAL cc_start: 0.7848 (t) cc_final: 0.7392 (p) REVERT: C 61 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8116 (mmtm) REVERT: C 76 ILE cc_start: 0.7428 (mm) cc_final: 0.7177 (tp) REVERT: C 82 MET cc_start: 0.7880 (tpp) cc_final: 0.6960 (tpp) REVERT: C 84 LYS cc_start: 0.9149 (ttmm) cc_final: 0.8878 (ttmm) REVERT: C 87 HIS cc_start: 0.8243 (t70) cc_final: 0.7539 (t-90) REVERT: C 90 PHE cc_start: 0.7838 (m-10) cc_final: 0.7283 (m-80) REVERT: C 91 TYR cc_start: 0.8032 (m-80) cc_final: 0.7515 (m-80) REVERT: C 105 LEU cc_start: 0.8086 (mm) cc_final: 0.7849 (mm) REVERT: C 107 GLU cc_start: 0.7284 (pm20) cc_final: 0.6701 (pm20) REVERT: C 111 ASN cc_start: 0.9032 (t0) cc_final: 0.8424 (t0) REVERT: C 115 ASN cc_start: 0.8520 (t0) cc_final: 0.8283 (t0) REVERT: C 117 GLU cc_start: 0.8445 (pp20) cc_final: 0.8157 (pp20) REVERT: C 119 MET cc_start: 0.8350 (ttm) cc_final: 0.8034 (ttm) REVERT: C 121 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 123 MET cc_start: 0.8205 (tpp) cc_final: 0.7241 (tpp) REVERT: C 127 PHE cc_start: 0.8004 (m-80) cc_final: 0.7331 (m-80) REVERT: C 140 LEU cc_start: 0.8879 (mt) cc_final: 0.8654 (mt) REVERT: C 151 ILE cc_start: 0.8037 (tt) cc_final: 0.7304 (tp) REVERT: C 153 LEU cc_start: 0.8306 (tp) cc_final: 0.8062 (tp) REVERT: C 164 PRO cc_start: 0.7672 (Cg_endo) cc_final: 0.7366 (Cg_exo) REVERT: C 166 TYR cc_start: 0.8002 (t80) cc_final: 0.7167 (t80) REVERT: C 167 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8060 (mm-30) REVERT: C 187 ASP cc_start: 0.8814 (m-30) cc_final: 0.8523 (m-30) REVERT: C 191 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8826 (ttpt) REVERT: C 196 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7493 (ttm170) REVERT: C 205 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 207 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 208 ILE cc_start: 0.8607 (mt) cc_final: 0.8402 (mt) REVERT: C 210 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8125 (ttp80) REVERT: C 211 ASP cc_start: 0.8184 (m-30) cc_final: 0.7641 (m-30) REVERT: C 212 ILE cc_start: 0.8802 (mt) cc_final: 0.8473 (mm) REVERT: C 213 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8316 (ttpt) REVERT: C 240 TYR cc_start: 0.7863 (t80) cc_final: 0.7354 (t80) REVERT: C 242 LEU cc_start: 0.8594 (mt) cc_final: 0.8320 (mt) REVERT: C 259 GLU cc_start: 0.8827 (tp30) cc_final: 0.8099 (tp30) REVERT: C 262 PHE cc_start: 0.8723 (m-10) cc_final: 0.8321 (m-10) REVERT: C 263 GLN cc_start: 0.8029 (mt0) cc_final: 0.7718 (mt0) REVERT: C 276 GLU cc_start: 0.8539 (tp30) cc_final: 0.7597 (tp30) REVERT: C 280 ASN cc_start: 0.8711 (m110) cc_final: 0.7899 (m-40) REVERT: C 282 ILE cc_start: 0.8720 (mt) cc_final: 0.8386 (mt) REVERT: C 283 MET cc_start: 0.8324 (mmm) cc_final: 0.7930 (mmm) REVERT: C 284 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8406 (mtpt) REVERT: C 289 ILE cc_start: 0.7984 (mp) cc_final: 0.7561 (mm) REVERT: C 290 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6939 (mtt90) REVERT: C 294 TYR cc_start: 0.7984 (m-80) cc_final: 0.7637 (m-80) REVERT: C 296 ASN cc_start: 0.7276 (p0) cc_final: 0.6704 (p0) REVERT: C 299 MET cc_start: 0.7944 (mmm) cc_final: 0.7539 (mmm) REVERT: C 305 MET cc_start: 0.6924 (mmm) cc_final: 0.6504 (mmm) REVERT: C 313 MET cc_start: 0.8189 (tpp) cc_final: 0.7164 (tpp) REVERT: C 314 GLN cc_start: 0.8526 (tt0) cc_final: 0.8266 (mt0) REVERT: C 316 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 317 ILE cc_start: 0.8794 (mm) cc_final: 0.8202 (mm) REVERT: C 328 LYS cc_start: 0.8487 (mttp) cc_final: 0.8243 (mttp) REVERT: C 361 GLU cc_start: 0.8670 (tp30) cc_final: 0.8133 (tp30) REVERT: D 12 ASN cc_start: 0.7202 (m-40) cc_final: 0.6988 (m-40) REVERT: D 24 ASP cc_start: 0.6547 (t0) cc_final: 0.6193 (t0) REVERT: D 33 SER cc_start: 0.8113 (p) cc_final: 0.7799 (p) REVERT: D 34 ILE cc_start: 0.8176 (mt) cc_final: 0.7492 (tt) REVERT: D 37 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7459 (tpp80) REVERT: D 41 GLN cc_start: 0.8025 (tp40) cc_final: 0.7662 (tm-30) REVERT: D 52 SER cc_start: 0.7694 (t) cc_final: 0.6960 (m) REVERT: D 62 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7693 (mtm-85) REVERT: D 67 LEU cc_start: 0.8153 (mt) cc_final: 0.7935 (mt) REVERT: D 68 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7585 (mmtt) REVERT: D 81 ASP cc_start: 0.8128 (m-30) cc_final: 0.7375 (m-30) REVERT: D 82 MET cc_start: 0.8267 (mmp) cc_final: 0.7796 (mmp) REVERT: D 84 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8561 (mtmt) REVERT: D 87 HIS cc_start: 0.8525 (t-90) cc_final: 0.7929 (t-90) REVERT: D 88 HIS cc_start: 0.8515 (t70) cc_final: 0.8044 (t-90) REVERT: D 91 TYR cc_start: 0.8285 (m-80) cc_final: 0.7384 (m-80) REVERT: D 92 ASN cc_start: 0.7827 (m110) cc_final: 0.7228 (m110) REVERT: D 99 GLU cc_start: 0.7661 (mp0) cc_final: 0.7360 (mp0) REVERT: D 116 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8232 (tpp-160) REVERT: D 119 MET cc_start: 0.8859 (ttm) cc_final: 0.8566 (ttm) REVERT: D 121 GLN cc_start: 0.8852 (pp30) cc_final: 0.8593 (pp30) REVERT: D 124 PHE cc_start: 0.7977 (m-80) cc_final: 0.7417 (m-80) REVERT: D 137 GLN cc_start: 0.8072 (mt0) cc_final: 0.7700 (mt0) REVERT: D 143 TYR cc_start: 0.6754 (m-10) cc_final: 0.6462 (m-80) REVERT: D 147 ARG cc_start: 0.7345 (mmt90) cc_final: 0.7104 (ttm110) REVERT: D 165 ILE cc_start: 0.8017 (mt) cc_final: 0.7802 (tt) REVERT: D 175 ILE cc_start: 0.8477 (pt) cc_final: 0.7769 (pt) REVERT: D 176 MET cc_start: 0.7129 (mmm) cc_final: 0.6805 (mmm) REVERT: D 187 ASP cc_start: 0.8760 (m-30) cc_final: 0.8414 (m-30) REVERT: D 196 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7563 (tpp80) REVERT: D 203 THR cc_start: 0.8023 (p) cc_final: 0.7144 (p) REVERT: D 207 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7315 (mm-30) REVERT: D 210 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7786 (ttp80) REVERT: D 211 ASP cc_start: 0.8490 (m-30) cc_final: 0.8161 (m-30) REVERT: D 213 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8489 (ttpt) REVERT: D 214 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7865 (mt-10) REVERT: D 215 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8774 (mmmt) REVERT: D 225 ASN cc_start: 0.8693 (m-40) cc_final: 0.8469 (m-40) REVERT: D 240 TYR cc_start: 0.7862 (t80) cc_final: 0.7411 (t80) REVERT: D 259 GLU cc_start: 0.8359 (tp30) cc_final: 0.7952 (tp30) REVERT: D 267 ILE cc_start: 0.8920 (mt) cc_final: 0.8429 (tp) REVERT: D 269 MET cc_start: 0.8200 (mmp) cc_final: 0.7926 (mmp) REVERT: D 276 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 279 TYR cc_start: 0.8033 (t80) cc_final: 0.7506 (t80) REVERT: D 283 MET cc_start: 0.8587 (mmp) cc_final: 0.8146 (mmp) REVERT: D 286 ASP cc_start: 0.8301 (t0) cc_final: 0.7814 (t0) REVERT: D 287 ILE cc_start: 0.8484 (tp) cc_final: 0.8112 (tt) REVERT: D 288 ASP cc_start: 0.8439 (m-30) cc_final: 0.7721 (m-30) REVERT: D 289 ILE cc_start: 0.8172 (pt) cc_final: 0.7858 (pt) REVERT: D 290 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7080 (mtt180) REVERT: D 292 ASP cc_start: 0.8605 (m-30) cc_final: 0.7517 (t0) REVERT: D 293 LEU cc_start: 0.9013 (mt) cc_final: 0.8635 (mt) REVERT: D 294 TYR cc_start: 0.8392 (m-80) cc_final: 0.7696 (m-80) REVERT: D 297 ASN cc_start: 0.7832 (m-40) cc_final: 0.7601 (m-40) REVERT: D 299 MET cc_start: 0.8140 (mmm) cc_final: 0.7885 (mmm) REVERT: D 305 MET cc_start: 0.7093 (mmp) cc_final: 0.6866 (mmm) REVERT: D 312 ARG cc_start: 0.8891 (tpt-90) cc_final: 0.7873 (tpt-90) REVERT: D 313 MET cc_start: 0.8504 (tpp) cc_final: 0.7636 (tpp) REVERT: D 314 GLN cc_start: 0.8982 (tt0) cc_final: 0.8713 (mm-40) REVERT: D 316 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8039 (mm-30) REVERT: D 320 LEU cc_start: 0.8816 (mt) cc_final: 0.8387 (mt) REVERT: D 352 PHE cc_start: 0.8645 (t80) cc_final: 0.8288 (t80) REVERT: D 356 TRP cc_start: 0.7117 (m100) cc_final: 0.6136 (m100) REVERT: D 371 HIS cc_start: 0.7716 (p90) cc_final: 0.7258 (p90) outliers start: 0 outliers final: 0 residues processed: 763 average time/residue: 0.3464 time to fit residues: 371.0247 Evaluate side-chains 706 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 18 optimal weight: 0.7980 chunk 133 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 398 ASN A 545 ASN B 89 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 128 ASN C 280 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 40 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088362 restraints weight = 42071.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092156 restraints weight = 25037.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094847 restraints weight = 16833.111| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15177 Z= 0.177 Angle : 0.663 11.300 20547 Z= 0.330 Chirality : 0.044 0.188 2251 Planarity : 0.005 0.059 2631 Dihedral : 8.915 172.222 2071 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1847 helix: 1.11 (0.18), residues: 839 sheet: -0.89 (0.29), residues: 313 loop : -0.06 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.005 0.001 HIS C 371 PHE 0.016 0.001 PHE B 125 TYR 0.034 0.001 TYR A 439 ARG 0.012 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 747 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7337 (mm-30) REVERT: A 102 TYR cc_start: 0.8117 (m-80) cc_final: 0.7902 (m-80) REVERT: A 107 LEU cc_start: 0.7387 (tp) cc_final: 0.6971 (tt) REVERT: A 119 TYR cc_start: 0.6834 (m-80) cc_final: 0.6570 (m-80) REVERT: A 130 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8244 (mm110) REVERT: A 132 MET cc_start: 0.6666 (ttm) cc_final: 0.5871 (ttm) REVERT: A 138 HIS cc_start: 0.5933 (t-170) cc_final: 0.5265 (t-90) REVERT: A 149 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8278 (pt0) REVERT: A 156 ASN cc_start: 0.7244 (p0) cc_final: 0.6798 (m-40) REVERT: A 174 LYS cc_start: 0.8861 (pttp) cc_final: 0.8496 (pttm) REVERT: A 179 TYR cc_start: 0.8386 (t80) cc_final: 0.8110 (t80) REVERT: A 180 PHE cc_start: 0.8622 (m-80) cc_final: 0.8241 (m-80) REVERT: A 220 PHE cc_start: 0.7486 (p90) cc_final: 0.6943 (p90) REVERT: A 223 TYR cc_start: 0.7844 (t80) cc_final: 0.7643 (t80) REVERT: A 239 MET cc_start: 0.6900 (mmp) cc_final: 0.6362 (mmp) REVERT: A 248 ARG cc_start: 0.8532 (tpp80) cc_final: 0.7937 (tpm170) REVERT: A 260 HIS cc_start: 0.7879 (m-70) cc_final: 0.7522 (m-70) REVERT: A 262 PHE cc_start: 0.8564 (m-80) cc_final: 0.8019 (m-80) REVERT: A 286 HIS cc_start: 0.7023 (t70) cc_final: 0.6606 (t-90) REVERT: A 304 GLU cc_start: 0.8209 (mp0) cc_final: 0.7930 (mp0) REVERT: A 309 ARG cc_start: 0.8857 (ppt170) cc_final: 0.8612 (ppt170) REVERT: A 312 CYS cc_start: 0.8608 (m) cc_final: 0.8135 (m) REVERT: A 317 ILE cc_start: 0.8626 (mt) cc_final: 0.7992 (mt) REVERT: A 322 GLN cc_start: 0.8762 (mt0) cc_final: 0.8498 (mp10) REVERT: A 327 ARG cc_start: 0.8573 (mpt180) cc_final: 0.8299 (mmt180) REVERT: A 354 HIS cc_start: 0.7735 (t-90) cc_final: 0.7309 (t70) REVERT: A 360 PHE cc_start: 0.8107 (t80) cc_final: 0.7905 (t80) REVERT: A 364 MET cc_start: 0.7854 (mtt) cc_final: 0.7622 (mtt) REVERT: A 371 MET cc_start: 0.9160 (mtm) cc_final: 0.8649 (mpp) REVERT: A 373 HIS cc_start: 0.8440 (t70) cc_final: 0.8027 (t70) REVERT: A 408 TYR cc_start: 0.8675 (t80) cc_final: 0.7927 (t80) REVERT: A 423 LEU cc_start: 0.7560 (mt) cc_final: 0.7016 (mt) REVERT: A 432 PHE cc_start: 0.7203 (p90) cc_final: 0.6954 (p90) REVERT: A 453 CYS cc_start: 0.8698 (p) cc_final: 0.8427 (p) REVERT: A 460 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8249 (ptpp) REVERT: A 468 HIS cc_start: 0.8235 (t-90) cc_final: 0.7588 (t-90) REVERT: A 475 GLU cc_start: 0.8421 (pp20) cc_final: 0.8197 (pp20) REVERT: A 478 MET cc_start: 0.8754 (mtm) cc_final: 0.8362 (mtm) REVERT: A 498 LEU cc_start: 0.9009 (mp) cc_final: 0.8401 (tt) REVERT: A 515 MET cc_start: 0.7280 (ttm) cc_final: 0.6707 (tpt) REVERT: A 517 LYS cc_start: 0.5415 (mtmm) cc_final: 0.4889 (mtmm) REVERT: A 525 GLN cc_start: 0.8501 (tp40) cc_final: 0.7490 (tp-100) REVERT: A 526 LYS cc_start: 0.9065 (tttt) cc_final: 0.8246 (tppt) REVERT: A 528 TYR cc_start: 0.8108 (m-10) cc_final: 0.7808 (m-80) REVERT: A 529 ASN cc_start: 0.8417 (m-40) cc_final: 0.7518 (m110) REVERT: A 532 LEU cc_start: 0.7864 (mt) cc_final: 0.7216 (mt) REVERT: A 537 LEU cc_start: 0.9033 (mp) cc_final: 0.8743 (mp) REVERT: A 538 PHE cc_start: 0.7961 (t80) cc_final: 0.7180 (t80) REVERT: A 555 ASP cc_start: 0.7905 (t0) cc_final: 0.7609 (t0) REVERT: A 556 LYS cc_start: 0.8629 (mttt) cc_final: 0.7833 (mttm) REVERT: A 558 GLU cc_start: 0.7785 (tt0) cc_final: 0.7363 (tm-30) REVERT: A 568 ASN cc_start: 0.8330 (t0) cc_final: 0.8041 (t0) REVERT: A 574 GLU cc_start: 0.8636 (tp30) cc_final: 0.8126 (pm20) REVERT: A 587 MET cc_start: 0.8551 (mmp) cc_final: 0.8171 (pmm) REVERT: A 633 LYS cc_start: 0.7411 (mtmm) cc_final: 0.6825 (mmtt) REVERT: A 637 HIS cc_start: 0.7981 (t-90) cc_final: 0.7444 (t-90) REVERT: A 641 ASN cc_start: 0.8808 (m110) cc_final: 0.8427 (m-40) REVERT: A 643 LEU cc_start: 0.8885 (tp) cc_final: 0.8258 (tp) REVERT: A 647 MET cc_start: 0.8702 (mmm) cc_final: 0.8134 (mmm) REVERT: A 650 LEU cc_start: 0.8744 (mm) cc_final: 0.8336 (pp) REVERT: A 657 TYR cc_start: 0.6607 (m-80) cc_final: 0.5973 (m-80) REVERT: A 666 PHE cc_start: 0.8255 (m-10) cc_final: 0.7921 (m-10) REVERT: A 682 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8344 (ptt-90) REVERT: A 689 THR cc_start: 0.9028 (p) cc_final: 0.8800 (p) REVERT: A 741 TYR cc_start: 0.8558 (p90) cc_final: 0.7846 (p90) REVERT: A 750 PHE cc_start: 0.8890 (m-10) cc_final: 0.8536 (m-10) REVERT: A 757 TYR cc_start: 0.8976 (t80) cc_final: 0.8550 (t80) REVERT: B 35 ILE cc_start: 0.8513 (mt) cc_final: 0.7965 (tp) REVERT: B 48 MET cc_start: 0.7140 (mmp) cc_final: 0.6663 (tpp) REVERT: B 54 TYR cc_start: 0.8073 (m-80) cc_final: 0.7437 (m-10) REVERT: B 58 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7963 (tt0) REVERT: B 83 MET cc_start: 0.8243 (tpp) cc_final: 0.7773 (tpp) REVERT: B 84 GLU cc_start: 0.8789 (tt0) cc_final: 0.8335 (tm-30) REVERT: B 85 LYS cc_start: 0.9130 (mttm) cc_final: 0.8894 (mttm) REVERT: B 101 GLU cc_start: 0.8344 (pm20) cc_final: 0.8126 (pm20) REVERT: B 106 LEU cc_start: 0.8009 (mt) cc_final: 0.7789 (mt) REVERT: B 114 LYS cc_start: 0.8492 (ptmm) cc_final: 0.7553 (ptmm) REVERT: B 120 MET cc_start: 0.8471 (ttm) cc_final: 0.7878 (tmm) REVERT: B 121 THR cc_start: 0.8632 (p) cc_final: 0.8019 (p) REVERT: B 124 MET cc_start: 0.8393 (tpp) cc_final: 0.7718 (tpp) REVERT: B 128 PHE cc_start: 0.8167 (m-80) cc_final: 0.7357 (m-80) REVERT: B 133 MET cc_start: 0.7501 (ttp) cc_final: 0.6838 (ttp) REVERT: B 134 TYR cc_start: 0.7222 (t80) cc_final: 0.6877 (t80) REVERT: B 148 ARG cc_start: 0.6462 (mpt-90) cc_final: 0.6220 (mpt-90) REVERT: B 155 ASP cc_start: 0.6707 (t0) cc_final: 0.6396 (t0) REVERT: B 163 ASN cc_start: 0.8116 (t0) cc_final: 0.7594 (t0) REVERT: B 167 TYR cc_start: 0.8099 (t80) cc_final: 0.7465 (t80) REVERT: B 168 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 176 ILE cc_start: 0.8171 (mt) cc_final: 0.7940 (tp) REVERT: B 179 LEU cc_start: 0.6742 (tp) cc_final: 0.6483 (tp) REVERT: B 184 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7874 (ttm110) REVERT: B 186 LEU cc_start: 0.8678 (mt) cc_final: 0.8472 (mt) REVERT: B 192 LYS cc_start: 0.8283 (ptmt) cc_final: 0.8000 (ptmt) REVERT: B 203 THR cc_start: 0.8015 (t) cc_final: 0.7752 (p) REVERT: B 207 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8061 (ttm-80) REVERT: B 208 GLU cc_start: 0.8752 (tp30) cc_final: 0.8169 (pt0) REVERT: B 214 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8487 (ttpt) REVERT: B 216 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8522 (mmmm) REVERT: B 219 TYR cc_start: 0.7488 (p90) cc_final: 0.7204 (p90) REVERT: B 226 ASN cc_start: 0.8392 (t0) cc_final: 0.8126 (t0) REVERT: B 230 THR cc_start: 0.8464 (m) cc_final: 0.8133 (p) REVERT: B 256 PHE cc_start: 0.8437 (p90) cc_final: 0.8233 (p90) REVERT: B 263 PHE cc_start: 0.8618 (m-80) cc_final: 0.7769 (m-80) REVERT: B 264 GLN cc_start: 0.8612 (tp-100) cc_final: 0.7531 (mt0) REVERT: B 267 PHE cc_start: 0.8309 (m-10) cc_final: 0.7791 (m-10) REVERT: B 277 GLU cc_start: 0.8421 (tp30) cc_final: 0.8103 (tp30) REVERT: B 292 LYS cc_start: 0.8560 (pttm) cc_final: 0.8202 (pttm) REVERT: B 293 ASP cc_start: 0.8753 (m-30) cc_final: 0.8492 (m-30) REVERT: B 300 MET cc_start: 0.7884 (mmm) cc_final: 0.7628 (mmm) REVERT: B 306 MET cc_start: 0.7377 (mmt) cc_final: 0.7138 (mmt) REVERT: B 310 ILE cc_start: 0.8807 (tt) cc_final: 0.8191 (mm) REVERT: B 313 ARG cc_start: 0.8899 (tpt-90) cc_final: 0.8351 (tpp-160) REVERT: B 314 MET cc_start: 0.8428 (tpt) cc_final: 0.7820 (mmm) REVERT: B 316 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8617 (ptpt) REVERT: B 326 MET cc_start: 0.7215 (mmp) cc_final: 0.6961 (mmm) REVERT: B 329 LYS cc_start: 0.7357 (tmtt) cc_final: 0.7001 (tmtt) REVERT: B 335 GLU cc_start: 0.8036 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 338 TYR cc_start: 0.8019 (m-80) cc_final: 0.7263 (m-80) REVERT: B 351 SER cc_start: 0.8305 (t) cc_final: 0.7419 (t) REVERT: B 353 PHE cc_start: 0.8322 (t80) cc_final: 0.7993 (t80) REVERT: B 357 TRP cc_start: 0.6052 (m100) cc_final: 0.5337 (m-10) REVERT: B 358 ILE cc_start: 0.8041 (mm) cc_final: 0.7834 (mp) REVERT: B 360 LYS cc_start: 0.8125 (tptp) cc_final: 0.7475 (tptp) REVERT: B 364 ASP cc_start: 0.7944 (m-30) cc_final: 0.7245 (m-30) REVERT: B 372 HIS cc_start: 0.7912 (m-70) cc_final: 0.7057 (m-70) REVERT: C 9 VAL cc_start: 0.8369 (p) cc_final: 0.8162 (p) REVERT: C 37 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: C 44 MET cc_start: 0.8584 (ppp) cc_final: 0.7962 (ppp) REVERT: C 50 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8469 (mtmt) REVERT: C 54 VAL cc_start: 0.7838 (t) cc_final: 0.7458 (p) REVERT: C 61 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8111 (mmtm) REVERT: C 76 ILE cc_start: 0.7256 (mm) cc_final: 0.6926 (tp) REVERT: C 82 MET cc_start: 0.7893 (tpp) cc_final: 0.7005 (tpp) REVERT: C 83 GLU cc_start: 0.8755 (pp20) cc_final: 0.8479 (pp20) REVERT: C 84 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8829 (ttmm) REVERT: C 87 HIS cc_start: 0.8267 (t70) cc_final: 0.7449 (t-90) REVERT: C 90 PHE cc_start: 0.7802 (m-10) cc_final: 0.7119 (m-10) REVERT: C 91 TYR cc_start: 0.8036 (m-80) cc_final: 0.7505 (m-80) REVERT: C 99 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7354 (mm-30) REVERT: C 105 LEU cc_start: 0.8081 (mm) cc_final: 0.7865 (mm) REVERT: C 111 ASN cc_start: 0.8981 (t0) cc_final: 0.8384 (t0) REVERT: C 113 LYS cc_start: 0.8691 (mtmt) cc_final: 0.7821 (mtmt) REVERT: C 115 ASN cc_start: 0.8580 (t0) cc_final: 0.8280 (t0) REVERT: C 116 ARG cc_start: 0.8393 (ttm110) cc_final: 0.7921 (ttm110) REVERT: C 117 GLU cc_start: 0.8375 (pp20) cc_final: 0.8081 (pp20) REVERT: C 119 MET cc_start: 0.8394 (ttm) cc_final: 0.8125 (ttm) REVERT: C 121 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 123 MET cc_start: 0.8243 (tpp) cc_final: 0.7258 (tpp) REVERT: C 127 PHE cc_start: 0.7975 (m-80) cc_final: 0.7229 (m-80) REVERT: C 140 LEU cc_start: 0.8870 (mt) cc_final: 0.8613 (mt) REVERT: C 151 ILE cc_start: 0.7902 (tt) cc_final: 0.7128 (tp) REVERT: C 164 PRO cc_start: 0.7670 (Cg_endo) cc_final: 0.7355 (Cg_exo) REVERT: C 166 TYR cc_start: 0.7981 (t80) cc_final: 0.7105 (t80) REVERT: C 167 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 177 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7679 (tpp80) REVERT: C 187 ASP cc_start: 0.8887 (m-30) cc_final: 0.8583 (m-30) REVERT: C 192 ILE cc_start: 0.8605 (mm) cc_final: 0.7904 (pt) REVERT: C 194 THR cc_start: 0.8161 (m) cc_final: 0.7910 (p) REVERT: C 205 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 207 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 210 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8110 (ttp80) REVERT: C 211 ASP cc_start: 0.8164 (m-30) cc_final: 0.7540 (m-30) REVERT: C 212 ILE cc_start: 0.8788 (mt) cc_final: 0.8587 (mm) REVERT: C 213 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8310 (ttpt) REVERT: C 240 TYR cc_start: 0.7863 (t80) cc_final: 0.7371 (t80) REVERT: C 242 LEU cc_start: 0.8838 (mt) cc_final: 0.8155 (mt) REVERT: C 252 ASN cc_start: 0.8431 (p0) cc_final: 0.7687 (p0) REVERT: C 256 ARG cc_start: 0.8527 (mtp180) cc_final: 0.7894 (mtp180) REVERT: C 259 GLU cc_start: 0.8777 (tp30) cc_final: 0.8120 (tp30) REVERT: C 262 PHE cc_start: 0.8689 (m-10) cc_final: 0.8120 (m-10) REVERT: C 263 GLN cc_start: 0.8036 (mt0) cc_final: 0.7732 (mt0) REVERT: C 276 GLU cc_start: 0.8540 (tp30) cc_final: 0.7755 (tp30) REVERT: C 279 TYR cc_start: 0.8569 (t80) cc_final: 0.8191 (t80) REVERT: C 280 ASN cc_start: 0.8730 (m-40) cc_final: 0.8111 (m-40) REVERT: C 282 ILE cc_start: 0.8706 (mt) cc_final: 0.8308 (mt) REVERT: C 283 MET cc_start: 0.8312 (mmm) cc_final: 0.7771 (mmm) REVERT: C 284 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8401 (mtpt) REVERT: C 286 ASP cc_start: 0.8512 (t70) cc_final: 0.8280 (t70) REVERT: C 289 ILE cc_start: 0.8003 (mp) cc_final: 0.7616 (mm) REVERT: C 290 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6953 (mtt90) REVERT: C 294 TYR cc_start: 0.7944 (m-80) cc_final: 0.7616 (m-80) REVERT: C 296 ASN cc_start: 0.7275 (p0) cc_final: 0.6699 (p0) REVERT: C 299 MET cc_start: 0.7855 (mmm) cc_final: 0.7574 (mmm) REVERT: C 305 MET cc_start: 0.7005 (mmm) cc_final: 0.6653 (mmm) REVERT: C 313 MET cc_start: 0.8165 (tpp) cc_final: 0.7144 (tpp) REVERT: C 314 GLN cc_start: 0.8488 (tt0) cc_final: 0.8156 (mt0) REVERT: C 316 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 317 ILE cc_start: 0.8769 (mm) cc_final: 0.8175 (mm) REVERT: C 325 MET cc_start: 0.7573 (tpt) cc_final: 0.7136 (tpt) REVERT: C 328 LYS cc_start: 0.8462 (mttp) cc_final: 0.8205 (mttp) REVERT: C 340 TRP cc_start: 0.6846 (t60) cc_final: 0.6341 (t60) REVERT: C 361 GLU cc_start: 0.8669 (tp30) cc_final: 0.8132 (tp30) REVERT: D 24 ASP cc_start: 0.6556 (t0) cc_final: 0.6201 (t0) REVERT: D 34 ILE cc_start: 0.8174 (mt) cc_final: 0.7378 (tt) REVERT: D 39 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.7223 (ptt-90) REVERT: D 41 GLN cc_start: 0.8114 (tp40) cc_final: 0.7641 (tm-30) REVERT: D 50 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7750 (mtmm) REVERT: D 52 SER cc_start: 0.7742 (t) cc_final: 0.6809 (p) REVERT: D 62 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7384 (mtm-85) REVERT: D 64 ILE cc_start: 0.8199 (tp) cc_final: 0.7489 (tp) REVERT: D 68 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7607 (mmtt) REVERT: D 81 ASP cc_start: 0.8143 (m-30) cc_final: 0.7361 (m-30) REVERT: D 84 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8548 (mtmt) REVERT: D 87 HIS cc_start: 0.8498 (t-90) cc_final: 0.7914 (t-90) REVERT: D 88 HIS cc_start: 0.8566 (t70) cc_final: 0.8029 (t-90) REVERT: D 91 TYR cc_start: 0.8365 (m-80) cc_final: 0.7400 (m-80) REVERT: D 92 ASN cc_start: 0.7933 (m110) cc_final: 0.7368 (m110) REVERT: D 119 MET cc_start: 0.8858 (ttm) cc_final: 0.8559 (ttm) REVERT: D 121 GLN cc_start: 0.8833 (pp30) cc_final: 0.8558 (pp30) REVERT: D 124 PHE cc_start: 0.7959 (m-80) cc_final: 0.7430 (m-80) REVERT: D 143 TYR cc_start: 0.6924 (m-10) cc_final: 0.6604 (m-80) REVERT: D 147 ARG cc_start: 0.7377 (mmt90) cc_final: 0.7118 (ttm110) REVERT: D 155 SER cc_start: 0.6098 (p) cc_final: 0.5747 (p) REVERT: D 165 ILE cc_start: 0.8018 (mt) cc_final: 0.7749 (tt) REVERT: D 175 ILE cc_start: 0.8505 (pt) cc_final: 0.7884 (pt) REVERT: D 176 MET cc_start: 0.7075 (mmm) cc_final: 0.6721 (mmm) REVERT: D 177 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7318 (ttm170) REVERT: D 187 ASP cc_start: 0.8737 (m-30) cc_final: 0.8490 (m-30) REVERT: D 196 ARG cc_start: 0.7961 (tpp80) cc_final: 0.7533 (tpp80) REVERT: D 203 THR cc_start: 0.7837 (p) cc_final: 0.7033 (p) REVERT: D 207 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7270 (mm-30) REVERT: D 208 ILE cc_start: 0.8705 (mt) cc_final: 0.8351 (mm) REVERT: D 210 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7785 (ttp80) REVERT: D 211 ASP cc_start: 0.8496 (m-30) cc_final: 0.8086 (m-30) REVERT: D 213 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8467 (ttpt) REVERT: D 214 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 215 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8765 (mmmt) REVERT: D 216 LEU cc_start: 0.7985 (mm) cc_final: 0.7735 (mm) REVERT: D 225 ASN cc_start: 0.8724 (m-40) cc_final: 0.8501 (m-40) REVERT: D 240 TYR cc_start: 0.7813 (t80) cc_final: 0.7385 (t80) REVERT: D 254 ARG cc_start: 0.7606 (ptm160) cc_final: 0.7142 (ttp-170) REVERT: D 259 GLU cc_start: 0.8302 (tp30) cc_final: 0.7840 (tp30) REVERT: D 267 ILE cc_start: 0.9014 (mt) cc_final: 0.8489 (tp) REVERT: D 269 MET cc_start: 0.8111 (mmp) cc_final: 0.7871 (mmp) REVERT: D 279 TYR cc_start: 0.8016 (t80) cc_final: 0.7532 (t80) REVERT: D 283 MET cc_start: 0.8590 (mmp) cc_final: 0.8150 (mmp) REVERT: D 286 ASP cc_start: 0.8357 (t0) cc_final: 0.7866 (t0) REVERT: D 287 ILE cc_start: 0.8430 (tp) cc_final: 0.8101 (tt) REVERT: D 288 ASP cc_start: 0.8349 (m-30) cc_final: 0.7663 (m-30) REVERT: D 289 ILE cc_start: 0.8164 (pt) cc_final: 0.7845 (pt) REVERT: D 290 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7065 (mtt180) REVERT: D 292 ASP cc_start: 0.8610 (m-30) cc_final: 0.7495 (t0) REVERT: D 293 LEU cc_start: 0.8997 (mt) cc_final: 0.8601 (mt) REVERT: D 294 TYR cc_start: 0.8454 (m-80) cc_final: 0.7676 (m-80) REVERT: D 297 ASN cc_start: 0.7774 (m-40) cc_final: 0.7548 (m-40) REVERT: D 298 VAL cc_start: 0.8452 (t) cc_final: 0.7873 (t) REVERT: D 299 MET cc_start: 0.8127 (mmm) cc_final: 0.7921 (mmm) REVERT: D 305 MET cc_start: 0.6992 (mmp) cc_final: 0.6753 (mmm) REVERT: D 312 ARG cc_start: 0.8864 (tpt-90) cc_final: 0.8619 (tpt-90) REVERT: D 316 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8496 (pt0) REVERT: D 320 LEU cc_start: 0.8811 (mt) cc_final: 0.8384 (mt) REVERT: D 334 GLU cc_start: 0.8233 (mp0) cc_final: 0.7980 (pm20) REVERT: D 352 PHE cc_start: 0.8562 (t80) cc_final: 0.8215 (t80) REVERT: D 356 TRP cc_start: 0.7042 (m100) cc_final: 0.6022 (m100) REVERT: D 371 HIS cc_start: 0.7706 (p90) cc_final: 0.7244 (p90) outliers start: 1 outliers final: 0 residues processed: 747 average time/residue: 0.3287 time to fit residues: 337.9887 Evaluate side-chains 710 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 176 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 49 optimal weight: 0.0570 chunk 132 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 89 HIS ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 101 HIS D 137 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086030 restraints weight = 42545.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089852 restraints weight = 25137.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092500 restraints weight = 16835.568| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15177 Z= 0.226 Angle : 0.696 9.790 20547 Z= 0.353 Chirality : 0.045 0.189 2251 Planarity : 0.005 0.059 2631 Dihedral : 9.041 173.055 2071 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1847 helix: 0.91 (0.18), residues: 841 sheet: -0.85 (0.29), residues: 298 loop : -0.19 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 79 HIS 0.025 0.001 HIS D 73 PHE 0.014 0.001 PHE B 125 TYR 0.034 0.002 TYR A 439 ARG 0.009 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9095 (tt0) cc_final: 0.8871 (mp0) REVERT: A 20 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7453 (mm-30) REVERT: A 90 ARG cc_start: 0.8584 (ptm-80) cc_final: 0.8180 (ttp80) REVERT: A 92 ARG cc_start: 0.8413 (mmp-170) cc_final: 0.7958 (mmp80) REVERT: A 110 ILE cc_start: 0.7573 (mp) cc_final: 0.7015 (tp) REVERT: A 125 ASN cc_start: 0.9152 (m110) cc_final: 0.8908 (m110) REVERT: A 132 MET cc_start: 0.6881 (ttm) cc_final: 0.6071 (ttm) REVERT: A 138 HIS cc_start: 0.5850 (t-170) cc_final: 0.5374 (t-90) REVERT: A 148 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8136 (mtmm) REVERT: A 149 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7987 (mm110) REVERT: A 156 ASN cc_start: 0.7426 (p0) cc_final: 0.6952 (t0) REVERT: A 174 LYS cc_start: 0.8906 (pttp) cc_final: 0.8525 (ptpp) REVERT: A 179 TYR cc_start: 0.8366 (t80) cc_final: 0.8103 (t80) REVERT: A 180 PHE cc_start: 0.8647 (m-80) cc_final: 0.8280 (m-80) REVERT: A 210 LYS cc_start: 0.7356 (tttm) cc_final: 0.6991 (ttpt) REVERT: A 219 ARG cc_start: 0.6872 (mmm160) cc_final: 0.5857 (mmm160) REVERT: A 220 PHE cc_start: 0.7426 (p90) cc_final: 0.6797 (p90) REVERT: A 239 MET cc_start: 0.6901 (mmp) cc_final: 0.6595 (mmp) REVERT: A 260 HIS cc_start: 0.7871 (m-70) cc_final: 0.7570 (m-70) REVERT: A 262 PHE cc_start: 0.8590 (m-80) cc_final: 0.8068 (m-80) REVERT: A 286 HIS cc_start: 0.7235 (t70) cc_final: 0.6828 (t-90) REVERT: A 304 GLU cc_start: 0.8255 (mp0) cc_final: 0.7988 (mp0) REVERT: A 309 ARG cc_start: 0.8830 (ppt170) cc_final: 0.8599 (ppt170) REVERT: A 312 CYS cc_start: 0.8535 (m) cc_final: 0.8293 (m) REVERT: A 317 ILE cc_start: 0.8651 (mt) cc_final: 0.8370 (mm) REVERT: A 327 ARG cc_start: 0.8596 (mpt180) cc_final: 0.8214 (mmt-90) REVERT: A 370 GLU cc_start: 0.8372 (tt0) cc_final: 0.7984 (tm-30) REVERT: A 371 MET cc_start: 0.9184 (mtm) cc_final: 0.8358 (mtp) REVERT: A 373 HIS cc_start: 0.8467 (t70) cc_final: 0.8081 (t70) REVERT: A 408 TYR cc_start: 0.8715 (t80) cc_final: 0.7956 (t80) REVERT: A 423 LEU cc_start: 0.7578 (mt) cc_final: 0.7297 (mm) REVERT: A 460 LYS cc_start: 0.8476 (mtmm) cc_final: 0.8245 (ptpp) REVERT: A 468 HIS cc_start: 0.8346 (t-90) cc_final: 0.7650 (t-90) REVERT: A 475 GLU cc_start: 0.8457 (pp20) cc_final: 0.8218 (pp20) REVERT: A 478 MET cc_start: 0.8727 (mtm) cc_final: 0.8338 (mtm) REVERT: A 498 LEU cc_start: 0.9032 (mp) cc_final: 0.8448 (tt) REVERT: A 510 ASP cc_start: 0.8926 (m-30) cc_final: 0.8575 (p0) REVERT: A 515 MET cc_start: 0.7331 (ttm) cc_final: 0.6808 (tpt) REVERT: A 520 ASP cc_start: 0.8451 (p0) cc_final: 0.8196 (m-30) REVERT: A 525 GLN cc_start: 0.8493 (tp40) cc_final: 0.7478 (tp-100) REVERT: A 526 LYS cc_start: 0.9040 (tttt) cc_final: 0.8255 (tppt) REVERT: A 528 TYR cc_start: 0.8170 (m-10) cc_final: 0.7931 (m-80) REVERT: A 529 ASN cc_start: 0.8509 (m-40) cc_final: 0.7560 (m110) REVERT: A 537 LEU cc_start: 0.9035 (mp) cc_final: 0.8734 (mp) REVERT: A 542 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.8153 (ttp80) REVERT: A 549 ILE cc_start: 0.7575 (tt) cc_final: 0.7288 (tt) REVERT: A 556 LYS cc_start: 0.8616 (mttt) cc_final: 0.8127 (mttm) REVERT: A 558 GLU cc_start: 0.7836 (tt0) cc_final: 0.7396 (tm-30) REVERT: A 568 ASN cc_start: 0.8376 (t0) cc_final: 0.8081 (t0) REVERT: A 574 GLU cc_start: 0.8750 (tp30) cc_final: 0.8130 (pm20) REVERT: A 587 MET cc_start: 0.8527 (mmp) cc_final: 0.8139 (pmm) REVERT: A 633 LYS cc_start: 0.7461 (mtmm) cc_final: 0.6776 (mmtm) REVERT: A 637 HIS cc_start: 0.8242 (t-90) cc_final: 0.7594 (t-90) REVERT: A 638 GLN cc_start: 0.8961 (pt0) cc_final: 0.8570 (pt0) REVERT: A 641 ASN cc_start: 0.8936 (m110) cc_final: 0.8492 (m110) REVERT: A 643 LEU cc_start: 0.8974 (tp) cc_final: 0.8534 (mt) REVERT: A 647 MET cc_start: 0.8763 (mmm) cc_final: 0.8206 (mmm) REVERT: A 650 LEU cc_start: 0.8753 (mm) cc_final: 0.8322 (pp) REVERT: A 657 TYR cc_start: 0.6649 (m-80) cc_final: 0.6030 (m-80) REVERT: A 666 PHE cc_start: 0.8301 (m-10) cc_final: 0.7953 (m-10) REVERT: A 682 ARG cc_start: 0.8708 (ptt-90) cc_final: 0.8369 (ptt-90) REVERT: A 741 TYR cc_start: 0.8453 (p90) cc_final: 0.7855 (p90) REVERT: A 750 PHE cc_start: 0.8901 (m-10) cc_final: 0.8598 (m-10) REVERT: A 757 TYR cc_start: 0.9027 (t80) cc_final: 0.8605 (t80) REVERT: B 32 PHE cc_start: 0.7968 (p90) cc_final: 0.7680 (p90) REVERT: B 35 ILE cc_start: 0.8622 (mt) cc_final: 0.8005 (tp) REVERT: B 48 MET cc_start: 0.7412 (mmp) cc_final: 0.6836 (tpp) REVERT: B 54 TYR cc_start: 0.8040 (m-80) cc_final: 0.7670 (m-10) REVERT: B 55 VAL cc_start: 0.8472 (t) cc_final: 0.7684 (p) REVERT: B 58 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8037 (pt0) REVERT: B 62 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8270 (mmtm) REVERT: B 82 ASP cc_start: 0.8475 (m-30) cc_final: 0.8061 (m-30) REVERT: B 83 MET cc_start: 0.8193 (tpp) cc_final: 0.7787 (tpp) REVERT: B 84 GLU cc_start: 0.8787 (tt0) cc_final: 0.8349 (tm-30) REVERT: B 85 LYS cc_start: 0.9130 (mttm) cc_final: 0.8929 (mttm) REVERT: B 100 GLU cc_start: 0.8435 (mp0) cc_final: 0.8225 (mp0) REVERT: B 101 GLU cc_start: 0.8304 (pm20) cc_final: 0.8058 (pm20) REVERT: B 108 GLU cc_start: 0.6829 (pp20) cc_final: 0.6297 (pp20) REVERT: B 114 LYS cc_start: 0.8532 (ptmm) cc_final: 0.7969 (ptmm) REVERT: B 117 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7730 (ttt-90) REVERT: B 118 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7042 (mm-30) REVERT: B 120 MET cc_start: 0.8548 (ttm) cc_final: 0.8006 (tmm) REVERT: B 121 THR cc_start: 0.8681 (p) cc_final: 0.8114 (p) REVERT: B 124 MET cc_start: 0.8350 (tpp) cc_final: 0.7739 (tpp) REVERT: B 128 PHE cc_start: 0.8161 (m-80) cc_final: 0.7397 (m-80) REVERT: B 133 MET cc_start: 0.7549 (ttp) cc_final: 0.6976 (ttp) REVERT: B 134 TYR cc_start: 0.7268 (t80) cc_final: 0.6884 (t80) REVERT: B 163 ASN cc_start: 0.8065 (t0) cc_final: 0.7847 (t0) REVERT: B 184 ARG cc_start: 0.8288 (ttm170) cc_final: 0.7834 (ttm110) REVERT: B 192 LYS cc_start: 0.8290 (ptmt) cc_final: 0.8002 (ptmt) REVERT: B 207 ARG cc_start: 0.8659 (ttm170) cc_final: 0.8044 (ttm-80) REVERT: B 214 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8515 (ttpt) REVERT: B 216 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8563 (mmmm) REVERT: B 226 ASN cc_start: 0.8599 (t0) cc_final: 0.8148 (t0) REVERT: B 230 THR cc_start: 0.8448 (m) cc_final: 0.8136 (p) REVERT: B 263 PHE cc_start: 0.8609 (m-80) cc_final: 0.7943 (m-80) REVERT: B 264 GLN cc_start: 0.8585 (tp-100) cc_final: 0.7441 (mt0) REVERT: B 267 PHE cc_start: 0.8385 (m-10) cc_final: 0.7701 (m-10) REVERT: B 277 GLU cc_start: 0.8444 (tp30) cc_final: 0.8121 (tp30) REVERT: B 292 LYS cc_start: 0.8501 (pttm) cc_final: 0.8103 (pttm) REVERT: B 293 ASP cc_start: 0.8759 (m-30) cc_final: 0.8482 (m-30) REVERT: B 298 ASN cc_start: 0.7002 (m-40) cc_final: 0.6392 (m-40) REVERT: B 300 MET cc_start: 0.7866 (mmm) cc_final: 0.7637 (mmm) REVERT: B 306 MET cc_start: 0.7466 (mmt) cc_final: 0.7208 (mmt) REVERT: B 310 ILE cc_start: 0.8816 (tt) cc_final: 0.7608 (mm) REVERT: B 313 ARG cc_start: 0.8848 (tpt-90) cc_final: 0.8247 (tpp-160) REVERT: B 314 MET cc_start: 0.8494 (tpt) cc_final: 0.7787 (mmm) REVERT: B 316 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8568 (ptpt) REVERT: B 325 THR cc_start: 0.8727 (t) cc_final: 0.8344 (p) REVERT: B 326 MET cc_start: 0.7116 (mmp) cc_final: 0.6820 (mmm) REVERT: B 329 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6876 (tmtt) REVERT: B 335 GLU cc_start: 0.7907 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 338 TYR cc_start: 0.8196 (m-80) cc_final: 0.7352 (m-80) REVERT: B 351 SER cc_start: 0.8205 (t) cc_final: 0.7930 (t) REVERT: B 360 LYS cc_start: 0.8188 (tptp) cc_final: 0.7618 (tptp) REVERT: B 364 ASP cc_start: 0.7979 (m-30) cc_final: 0.7336 (m-30) REVERT: B 372 HIS cc_start: 0.8035 (m-70) cc_final: 0.7306 (m90) REVERT: C 39 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7571 (mtm-85) REVERT: C 50 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8408 (mtmt) REVERT: C 54 VAL cc_start: 0.7845 (t) cc_final: 0.7554 (p) REVERT: C 82 MET cc_start: 0.7934 (tpp) cc_final: 0.7113 (tpp) REVERT: C 83 GLU cc_start: 0.8760 (pp20) cc_final: 0.8483 (pp20) REVERT: C 84 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8796 (ttmm) REVERT: C 87 HIS cc_start: 0.8261 (t70) cc_final: 0.7491 (t-90) REVERT: C 90 PHE cc_start: 0.7866 (m-10) cc_final: 0.7307 (m-80) REVERT: C 91 TYR cc_start: 0.8027 (m-80) cc_final: 0.7511 (m-80) REVERT: C 105 LEU cc_start: 0.8106 (mm) cc_final: 0.7835 (mm) REVERT: C 111 ASN cc_start: 0.9088 (t0) cc_final: 0.8599 (t0) REVERT: C 113 LYS cc_start: 0.8682 (mtmt) cc_final: 0.7860 (mtmt) REVERT: C 116 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7883 (ttm110) REVERT: C 117 GLU cc_start: 0.8364 (pp20) cc_final: 0.8109 (pp20) REVERT: C 119 MET cc_start: 0.8392 (ttm) cc_final: 0.8141 (ttm) REVERT: C 123 MET cc_start: 0.8378 (tpp) cc_final: 0.7475 (tpp) REVERT: C 127 PHE cc_start: 0.8092 (m-80) cc_final: 0.7279 (m-80) REVERT: C 136 ILE cc_start: 0.8690 (mm) cc_final: 0.8014 (tp) REVERT: C 140 LEU cc_start: 0.8934 (mt) cc_final: 0.8700 (mt) REVERT: C 151 ILE cc_start: 0.7913 (tt) cc_final: 0.7076 (tp) REVERT: C 164 PRO cc_start: 0.7622 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: C 166 TYR cc_start: 0.8007 (t80) cc_final: 0.7068 (t80) REVERT: C 167 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 187 ASP cc_start: 0.8918 (m-30) cc_final: 0.8617 (m-30) REVERT: C 191 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8643 (ttpt) REVERT: C 194 THR cc_start: 0.8174 (m) cc_final: 0.7961 (p) REVERT: C 205 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 211 ASP cc_start: 0.8158 (m-30) cc_final: 0.7857 (m-30) REVERT: C 212 ILE cc_start: 0.8803 (mt) cc_final: 0.8504 (mm) REVERT: C 213 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8355 (ttpt) REVERT: C 225 ASN cc_start: 0.7927 (t0) cc_final: 0.7718 (t0) REVERT: C 240 TYR cc_start: 0.7839 (t80) cc_final: 0.7586 (t80) REVERT: C 242 LEU cc_start: 0.8432 (mt) cc_final: 0.8117 (mt) REVERT: C 259 GLU cc_start: 0.8789 (tp30) cc_final: 0.8280 (tp30) REVERT: C 262 PHE cc_start: 0.8732 (m-10) cc_final: 0.8350 (m-10) REVERT: C 263 GLN cc_start: 0.8068 (mt0) cc_final: 0.7724 (mt0) REVERT: C 276 GLU cc_start: 0.8546 (tp30) cc_final: 0.7619 (tp30) REVERT: C 279 TYR cc_start: 0.8563 (t80) cc_final: 0.8317 (t80) REVERT: C 280 ASN cc_start: 0.8726 (m-40) cc_final: 0.7912 (m-40) REVERT: C 282 ILE cc_start: 0.8708 (mt) cc_final: 0.8353 (mt) REVERT: C 283 MET cc_start: 0.8269 (mmm) cc_final: 0.7885 (mmm) REVERT: C 284 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8451 (mtpt) REVERT: C 286 ASP cc_start: 0.8543 (t70) cc_final: 0.8325 (t70) REVERT: C 289 ILE cc_start: 0.8073 (mp) cc_final: 0.7687 (mm) REVERT: C 294 TYR cc_start: 0.7973 (m-80) cc_final: 0.7654 (m-80) REVERT: C 296 ASN cc_start: 0.7411 (p0) cc_final: 0.6814 (p0) REVERT: C 305 MET cc_start: 0.7101 (mmm) cc_final: 0.6898 (mmm) REVERT: C 313 MET cc_start: 0.8160 (tpp) cc_final: 0.7170 (tpp) REVERT: C 314 GLN cc_start: 0.8535 (tt0) cc_final: 0.8227 (mt0) REVERT: C 316 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 317 ILE cc_start: 0.8799 (mm) cc_final: 0.8210 (mm) REVERT: C 361 GLU cc_start: 0.8711 (tp30) cc_final: 0.8317 (tm-30) REVERT: C 371 HIS cc_start: 0.7492 (m170) cc_final: 0.6895 (m-70) REVERT: D 24 ASP cc_start: 0.6624 (t0) cc_final: 0.6260 (t0) REVERT: D 34 ILE cc_start: 0.8128 (mt) cc_final: 0.7629 (mt) REVERT: D 41 GLN cc_start: 0.8007 (tp40) cc_final: 0.7632 (tm-30) REVERT: D 43 VAL cc_start: 0.8497 (m) cc_final: 0.8200 (p) REVERT: D 62 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7584 (mtm-85) REVERT: D 65 LEU cc_start: 0.8355 (mm) cc_final: 0.8065 (mm) REVERT: D 81 ASP cc_start: 0.8047 (m-30) cc_final: 0.7471 (m-30) REVERT: D 82 MET cc_start: 0.8069 (mmp) cc_final: 0.7861 (mmp) REVERT: D 84 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8507 (mtmt) REVERT: D 87 HIS cc_start: 0.8535 (t-90) cc_final: 0.7963 (t-90) REVERT: D 88 HIS cc_start: 0.8613 (t70) cc_final: 0.7979 (t-90) REVERT: D 91 TYR cc_start: 0.8381 (m-80) cc_final: 0.7422 (m-80) REVERT: D 92 ASN cc_start: 0.7968 (m110) cc_final: 0.7428 (m110) REVERT: D 105 LEU cc_start: 0.7645 (mm) cc_final: 0.7442 (mm) REVERT: D 116 ARG cc_start: 0.8231 (mmp-170) cc_final: 0.7694 (mmp-170) REVERT: D 119 MET cc_start: 0.8876 (ttm) cc_final: 0.8078 (ttm) REVERT: D 121 GLN cc_start: 0.8862 (pp30) cc_final: 0.8601 (pp30) REVERT: D 124 PHE cc_start: 0.7995 (m-80) cc_final: 0.7493 (m-80) REVERT: D 143 TYR cc_start: 0.6985 (m-10) cc_final: 0.6678 (m-80) REVERT: D 147 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7202 (mmm160) REVERT: D 155 SER cc_start: 0.6099 (p) cc_final: 0.5616 (t) REVERT: D 175 ILE cc_start: 0.8506 (pt) cc_final: 0.7809 (pt) REVERT: D 176 MET cc_start: 0.7055 (mmm) cc_final: 0.6751 (mmm) REVERT: D 187 ASP cc_start: 0.8745 (m-30) cc_final: 0.8419 (m-30) REVERT: D 191 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8602 (ttpt) REVERT: D 192 ILE cc_start: 0.8362 (tp) cc_final: 0.7940 (tp) REVERT: D 195 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6837 (mm-30) REVERT: D 203 THR cc_start: 0.7990 (p) cc_final: 0.7240 (p) REVERT: D 205 GLU cc_start: 0.8017 (pt0) cc_final: 0.7504 (pp20) REVERT: D 207 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7135 (mm-30) REVERT: D 210 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7766 (ttp80) REVERT: D 211 ASP cc_start: 0.8531 (m-30) cc_final: 0.8140 (m-30) REVERT: D 213 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8522 (ttpt) REVERT: D 214 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7935 (mt-10) REVERT: D 215 LYS cc_start: 0.8994 (mmpt) cc_final: 0.8735 (mmmt) REVERT: D 216 LEU cc_start: 0.7958 (mm) cc_final: 0.7717 (mm) REVERT: D 241 GLU cc_start: 0.7910 (pp20) cc_final: 0.7703 (pp20) REVERT: D 254 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7200 (ttp-170) REVERT: D 259 GLU cc_start: 0.8307 (tp30) cc_final: 0.7886 (tp30) REVERT: D 279 TYR cc_start: 0.8021 (t80) cc_final: 0.7506 (t80) REVERT: D 283 MET cc_start: 0.8587 (mmp) cc_final: 0.8173 (mmp) REVERT: D 286 ASP cc_start: 0.8288 (t0) cc_final: 0.7618 (t0) REVERT: D 288 ASP cc_start: 0.8317 (m-30) cc_final: 0.7665 (m-30) REVERT: D 289 ILE cc_start: 0.8250 (pt) cc_final: 0.7525 (mt) REVERT: D 290 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7067 (mtt90) REVERT: D 292 ASP cc_start: 0.8575 (m-30) cc_final: 0.7537 (t0) REVERT: D 293 LEU cc_start: 0.8999 (mt) cc_final: 0.8511 (mt) REVERT: D 294 TYR cc_start: 0.8458 (m-80) cc_final: 0.7742 (m-80) REVERT: D 298 VAL cc_start: 0.8433 (t) cc_final: 0.7879 (t) REVERT: D 299 MET cc_start: 0.8185 (mmm) cc_final: 0.7798 (mmm) REVERT: D 305 MET cc_start: 0.7259 (mmp) cc_final: 0.6916 (mmm) REVERT: D 312 ARG cc_start: 0.8823 (tpt-90) cc_final: 0.8446 (tpt-90) REVERT: D 314 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8694 (mm-40) REVERT: D 320 LEU cc_start: 0.8843 (mt) cc_final: 0.8455 (mt) REVERT: D 329 ILE cc_start: 0.8395 (mm) cc_final: 0.7332 (mm) REVERT: D 346 LEU cc_start: 0.8183 (tp) cc_final: 0.7841 (tp) REVERT: D 356 TRP cc_start: 0.7026 (m100) cc_final: 0.6641 (m100) REVERT: D 361 GLU cc_start: 0.8908 (mp0) cc_final: 0.8429 (pm20) REVERT: D 371 HIS cc_start: 0.7732 (p90) cc_final: 0.7302 (p90) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.3365 time to fit residues: 350.2785 Evaluate side-chains 714 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 714 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 398 ASN A 679 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 101 HIS C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.112415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086531 restraints weight = 42464.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090330 restraints weight = 25089.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092952 restraints weight = 16840.000| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.8086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15177 Z= 0.204 Angle : 0.709 9.767 20547 Z= 0.357 Chirality : 0.046 0.236 2251 Planarity : 0.005 0.055 2631 Dihedral : 9.034 175.724 2071 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1847 helix: 0.79 (0.18), residues: 848 sheet: -0.93 (0.29), residues: 282 loop : -0.29 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 79 HIS 0.006 0.001 HIS C 101 PHE 0.041 0.002 PHE D 352 TYR 0.028 0.001 TYR A 439 ARG 0.010 0.001 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3694 Ramachandran restraints generated. 1847 Oldfield, 0 Emsley, 1847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 759 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9082 (tt0) cc_final: 0.8835 (mp0) REVERT: A 20 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7438 (mm-30) REVERT: A 90 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8237 (ttp80) REVERT: A 92 ARG cc_start: 0.8424 (mmp-170) cc_final: 0.7266 (mtp85) REVERT: A 107 LEU cc_start: 0.7680 (tt) cc_final: 0.6869 (tp) REVERT: A 132 MET cc_start: 0.6759 (ttm) cc_final: 0.6005 (ttm) REVERT: A 138 HIS cc_start: 0.5913 (t-170) cc_final: 0.5194 (t-90) REVERT: A 149 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8147 (mm-40) REVERT: A 156 ASN cc_start: 0.7414 (p0) cc_final: 0.6964 (t0) REVERT: A 174 LYS cc_start: 0.8880 (pttp) cc_final: 0.8496 (ptpp) REVERT: A 179 TYR cc_start: 0.8332 (t80) cc_final: 0.8095 (t80) REVERT: A 180 PHE cc_start: 0.8626 (m-80) cc_final: 0.8300 (m-80) REVERT: A 203 MET cc_start: 0.9090 (ptp) cc_final: 0.8796 (mpp) REVERT: A 210 LYS cc_start: 0.7375 (tttm) cc_final: 0.6977 (ttpt) REVERT: A 211 THR cc_start: 0.8323 (p) cc_final: 0.8041 (p) REVERT: A 219 ARG cc_start: 0.6853 (mmm160) cc_final: 0.5863 (mmm160) REVERT: A 220 PHE cc_start: 0.7377 (p90) cc_final: 0.6695 (p90) REVERT: A 222 LYS cc_start: 0.7851 (tptp) cc_final: 0.7467 (tptt) REVERT: A 239 MET cc_start: 0.6866 (mmp) cc_final: 0.6457 (mmp) REVERT: A 244 LEU cc_start: 0.8209 (tp) cc_final: 0.7818 (tp) REVERT: A 248 ARG cc_start: 0.8532 (tpp80) cc_final: 0.7975 (tpm170) REVERT: A 260 HIS cc_start: 0.7907 (m-70) cc_final: 0.7621 (m-70) REVERT: A 262 PHE cc_start: 0.8548 (m-80) cc_final: 0.7996 (m-80) REVERT: A 286 HIS cc_start: 0.7265 (t70) cc_final: 0.6856 (t-90) REVERT: A 307 HIS cc_start: 0.8900 (m90) cc_final: 0.8665 (m90) REVERT: A 317 ILE cc_start: 0.8649 (mt) cc_final: 0.8436 (mm) REVERT: A 327 ARG cc_start: 0.8586 (mpt180) cc_final: 0.8127 (mmt-90) REVERT: A 329 LEU cc_start: 0.8683 (mt) cc_final: 0.8294 (pp) REVERT: A 370 GLU cc_start: 0.8361 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 371 MET cc_start: 0.9117 (mtm) cc_final: 0.8231 (mpp) REVERT: A 373 HIS cc_start: 0.8467 (t70) cc_final: 0.8095 (t70) REVERT: A 408 TYR cc_start: 0.8683 (t80) cc_final: 0.7891 (t80) REVERT: A 423 LEU cc_start: 0.7602 (mt) cc_final: 0.6994 (mt) REVERT: A 450 GLU cc_start: 0.8994 (mp0) cc_final: 0.8588 (pm20) REVERT: A 451 GLN cc_start: 0.8592 (mp10) cc_final: 0.8380 (mp10) REVERT: A 460 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8280 (ptpp) REVERT: A 468 HIS cc_start: 0.8345 (t-90) cc_final: 0.7624 (t-90) REVERT: A 478 MET cc_start: 0.8681 (mtm) cc_final: 0.8416 (mtm) REVERT: A 498 LEU cc_start: 0.8997 (mp) cc_final: 0.8462 (tt) REVERT: A 511 GLU cc_start: 0.8535 (tt0) cc_final: 0.8319 (tt0) REVERT: A 512 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 515 MET cc_start: 0.7276 (ttm) cc_final: 0.6732 (tpt) REVERT: A 520 ASP cc_start: 0.8452 (p0) cc_final: 0.7867 (m-30) REVERT: A 526 LYS cc_start: 0.9005 (tttt) cc_final: 0.8372 (tppt) REVERT: A 529 ASN cc_start: 0.8482 (m-40) cc_final: 0.8007 (m-40) REVERT: A 537 LEU cc_start: 0.9014 (mp) cc_final: 0.8685 (mp) REVERT: A 542 ARG cc_start: 0.8512 (tmm-80) cc_final: 0.8134 (ttp80) REVERT: A 556 LYS cc_start: 0.8617 (mttt) cc_final: 0.8110 (mttm) REVERT: A 558 GLU cc_start: 0.7836 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 564 PHE cc_start: 0.6899 (p90) cc_final: 0.6485 (p90) REVERT: A 568 ASN cc_start: 0.8324 (t0) cc_final: 0.8002 (t0) REVERT: A 587 MET cc_start: 0.8522 (mmp) cc_final: 0.8125 (pmm) REVERT: A 633 LYS cc_start: 0.7541 (mtmm) cc_final: 0.6979 (mmtm) REVERT: A 637 HIS cc_start: 0.8252 (t-90) cc_final: 0.7565 (t-90) REVERT: A 638 GLN cc_start: 0.8966 (pt0) cc_final: 0.8576 (pt0) REVERT: A 641 ASN cc_start: 0.8922 (m110) cc_final: 0.8423 (m110) REVERT: A 643 LEU cc_start: 0.8995 (tp) cc_final: 0.8218 (tp) REVERT: A 647 MET cc_start: 0.8688 (mmm) cc_final: 0.8113 (mmm) REVERT: A 650 LEU cc_start: 0.8710 (mm) cc_final: 0.8372 (pp) REVERT: A 657 TYR cc_start: 0.6653 (m-80) cc_final: 0.6040 (m-80) REVERT: A 666 PHE cc_start: 0.8320 (m-10) cc_final: 0.8023 (m-10) REVERT: A 682 ARG cc_start: 0.8690 (ptt-90) cc_final: 0.8348 (ptt-90) REVERT: A 689 THR cc_start: 0.9060 (p) cc_final: 0.8845 (p) REVERT: A 741 TYR cc_start: 0.8353 (p90) cc_final: 0.7683 (p90) REVERT: A 750 PHE cc_start: 0.8907 (m-10) cc_final: 0.8547 (m-10) REVERT: A 751 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8007 (mtp85) REVERT: A 757 TYR cc_start: 0.9009 (t80) cc_final: 0.8593 (t80) REVERT: B 32 PHE cc_start: 0.7909 (p90) cc_final: 0.7677 (p90) REVERT: B 35 ILE cc_start: 0.8462 (mt) cc_final: 0.7952 (tp) REVERT: B 48 MET cc_start: 0.7409 (mmp) cc_final: 0.6844 (tpp) REVERT: B 54 TYR cc_start: 0.8083 (m-80) cc_final: 0.7710 (m-10) REVERT: B 55 VAL cc_start: 0.8532 (t) cc_final: 0.7806 (p) REVERT: B 58 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8039 (pt0) REVERT: B 62 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8056 (mmtm) REVERT: B 83 MET cc_start: 0.8214 (tpp) cc_final: 0.7822 (tpp) REVERT: B 84 GLU cc_start: 0.8797 (tt0) cc_final: 0.8350 (tm-30) REVERT: B 93 ASN cc_start: 0.8134 (m110) cc_final: 0.7832 (m110) REVERT: B 100 GLU cc_start: 0.8406 (mp0) cc_final: 0.8098 (mp0) REVERT: B 101 GLU cc_start: 0.8330 (pm20) cc_final: 0.8120 (pm20) REVERT: B 108 GLU cc_start: 0.6691 (pp20) cc_final: 0.6417 (pp20) REVERT: B 111 LEU cc_start: 0.8423 (mt) cc_final: 0.8026 (mt) REVERT: B 114 LYS cc_start: 0.8474 (ptmm) cc_final: 0.7607 (ptmm) REVERT: B 117 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7775 (ttt-90) REVERT: B 120 MET cc_start: 0.8524 (ttm) cc_final: 0.7978 (tmm) REVERT: B 121 THR cc_start: 0.8635 (p) cc_final: 0.8158 (p) REVERT: B 124 MET cc_start: 0.8382 (tpp) cc_final: 0.7749 (tpp) REVERT: B 128 PHE cc_start: 0.8177 (m-80) cc_final: 0.7423 (m-80) REVERT: B 133 MET cc_start: 0.7624 (ttp) cc_final: 0.7054 (ttp) REVERT: B 134 TYR cc_start: 0.7225 (t80) cc_final: 0.6878 (t80) REVERT: B 144 TYR cc_start: 0.8492 (m-80) cc_final: 0.8279 (m-80) REVERT: B 163 ASN cc_start: 0.8008 (t0) cc_final: 0.7481 (t0) REVERT: B 176 ILE cc_start: 0.8202 (mt) cc_final: 0.7999 (tp) REVERT: B 184 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7827 (ttm110) REVERT: B 186 LEU cc_start: 0.8786 (mt) cc_final: 0.8574 (mt) REVERT: B 192 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7921 (ptmt) REVERT: B 207 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8084 (ttm-80) REVERT: B 208 GLU cc_start: 0.8182 (pt0) cc_final: 0.7868 (pt0) REVERT: B 211 ARG cc_start: 0.8916 (pmt-80) cc_final: 0.8530 (pmt-80) REVERT: B 212 ASP cc_start: 0.8708 (m-30) cc_final: 0.8252 (m-30) REVERT: B 214 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8549 (ttpt) REVERT: B 215 GLU cc_start: 0.8509 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 216 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8467 (mmmm) REVERT: B 226 ASN cc_start: 0.8576 (t0) cc_final: 0.8040 (t0) REVERT: B 230 THR cc_start: 0.8429 (m) cc_final: 0.8117 (p) REVERT: B 239 LYS cc_start: 0.8559 (mttt) cc_final: 0.8199 (mmmt) REVERT: B 260 GLU cc_start: 0.8496 (tp30) cc_final: 0.8288 (tp30) REVERT: B 263 PHE cc_start: 0.8632 (m-80) cc_final: 0.7883 (m-80) REVERT: B 264 GLN cc_start: 0.8566 (tp-100) cc_final: 0.7602 (mt0) REVERT: B 267 PHE cc_start: 0.8381 (m-10) cc_final: 0.7926 (m-10) REVERT: B 281 ASN cc_start: 0.8577 (t0) cc_final: 0.8218 (t0) REVERT: B 287 ASP cc_start: 0.7904 (t70) cc_final: 0.7671 (t70) REVERT: B 292 LYS cc_start: 0.8512 (pttm) cc_final: 0.8108 (pttm) REVERT: B 293 ASP cc_start: 0.8703 (m-30) cc_final: 0.8475 (m-30) REVERT: B 298 ASN cc_start: 0.7052 (m-40) cc_final: 0.6420 (m-40) REVERT: B 300 MET cc_start: 0.7855 (mmm) cc_final: 0.7625 (mmm) REVERT: B 306 MET cc_start: 0.7520 (mmt) cc_final: 0.7189 (mmt) REVERT: B 310 ILE cc_start: 0.8709 (tt) cc_final: 0.7887 (pt) REVERT: B 313 ARG cc_start: 0.8866 (tpt-90) cc_final: 0.8314 (tpp-160) REVERT: B 314 MET cc_start: 0.8400 (tpt) cc_final: 0.7747 (mmm) REVERT: B 316 LYS cc_start: 0.8875 (ptpt) cc_final: 0.8550 (ptpt) REVERT: B 325 THR cc_start: 0.8685 (t) cc_final: 0.8471 (p) REVERT: B 326 MET cc_start: 0.7077 (mmp) cc_final: 0.6768 (mmm) REVERT: B 329 LYS cc_start: 0.7492 (tmtt) cc_final: 0.6877 (tmtt) REVERT: B 335 GLU cc_start: 0.7962 (mm-30) cc_final: 0.6867 (mm-30) REVERT: B 338 TYR cc_start: 0.8141 (m-80) cc_final: 0.7316 (m-80) REVERT: B 355 GLN cc_start: 0.8587 (pp30) cc_final: 0.7893 (pp30) REVERT: B 356 MET cc_start: 0.8708 (mtt) cc_final: 0.7938 (mmm) REVERT: B 360 LYS cc_start: 0.8161 (tptp) cc_final: 0.7560 (tptp) REVERT: B 364 ASP cc_start: 0.8012 (m-30) cc_final: 0.7360 (m-30) REVERT: B 372 HIS cc_start: 0.8038 (m-70) cc_final: 0.6920 (m90) REVERT: C 37 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7328 (mmm-85) REVERT: C 39 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: C 44 MET cc_start: 0.8565 (ppp) cc_final: 0.8285 (ppp) REVERT: C 50 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8397 (mtmt) REVERT: C 54 VAL cc_start: 0.7798 (t) cc_final: 0.7243 (p) REVERT: C 61 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8208 (mmtm) REVERT: C 82 MET cc_start: 0.7915 (tpp) cc_final: 0.7102 (tpp) REVERT: C 83 GLU cc_start: 0.8749 (pp20) cc_final: 0.8472 (pp20) REVERT: C 84 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8828 (ttmm) REVERT: C 85 ILE cc_start: 0.8940 (mm) cc_final: 0.8645 (mp) REVERT: C 87 HIS cc_start: 0.8306 (t70) cc_final: 0.7543 (t-90) REVERT: C 90 PHE cc_start: 0.7830 (m-10) cc_final: 0.7249 (m-80) REVERT: C 91 TYR cc_start: 0.8071 (m-80) cc_final: 0.7515 (m-80) REVERT: C 105 LEU cc_start: 0.8085 (mm) cc_final: 0.7844 (mm) REVERT: C 111 ASN cc_start: 0.8719 (t0) cc_final: 0.8242 (t0) REVERT: C 113 LYS cc_start: 0.8733 (mtmt) cc_final: 0.7928 (mtmt) REVERT: C 116 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8046 (ttm110) REVERT: C 117 GLU cc_start: 0.8340 (pp20) cc_final: 0.8050 (pp20) REVERT: C 119 MET cc_start: 0.8390 (ttm) cc_final: 0.8145 (ttm) REVERT: C 121 GLN cc_start: 0.8799 (tm-30) cc_final: 0.7999 (tm-30) REVERT: C 123 MET cc_start: 0.8324 (tpp) cc_final: 0.7458 (tpp) REVERT: C 126 THR cc_start: 0.8287 (m) cc_final: 0.7740 (m) REVERT: C 127 PHE cc_start: 0.8049 (m-80) cc_final: 0.7254 (m-80) REVERT: C 136 ILE cc_start: 0.8717 (mm) cc_final: 0.7952 (tp) REVERT: C 140 LEU cc_start: 0.8890 (mt) cc_final: 0.8647 (mt) REVERT: C 164 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7268 (Cg_exo) REVERT: C 167 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 177 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7665 (tpp80) REVERT: C 187 ASP cc_start: 0.8876 (m-30) cc_final: 0.8573 (m-30) REVERT: C 205 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7602 (mt-10) REVERT: C 207 GLU cc_start: 0.8290 (pp20) cc_final: 0.7668 (pp20) REVERT: C 211 ASP cc_start: 0.8426 (m-30) cc_final: 0.7561 (m-30) REVERT: C 212 ILE cc_start: 0.8826 (mt) cc_final: 0.8538 (mm) REVERT: C 213 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8386 (ttpt) REVERT: C 225 ASN cc_start: 0.7956 (t0) cc_final: 0.7708 (t0) REVERT: C 240 TYR cc_start: 0.7792 (t80) cc_final: 0.7412 (t80) REVERT: C 242 LEU cc_start: 0.8422 (mt) cc_final: 0.8106 (mt) REVERT: C 254 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7495 (mtp85) REVERT: C 259 GLU cc_start: 0.8774 (tp30) cc_final: 0.8245 (tp30) REVERT: C 262 PHE cc_start: 0.8711 (m-10) cc_final: 0.8150 (m-10) REVERT: C 263 GLN cc_start: 0.8063 (mt0) cc_final: 0.7716 (mt0) REVERT: C 276 GLU cc_start: 0.8572 (tp30) cc_final: 0.7595 (tp30) REVERT: C 279 TYR cc_start: 0.8587 (t80) cc_final: 0.8272 (t80) REVERT: C 280 ASN cc_start: 0.8781 (m-40) cc_final: 0.7921 (m-40) REVERT: C 282 ILE cc_start: 0.8732 (mt) cc_final: 0.8339 (mt) REVERT: C 283 MET cc_start: 0.8305 (mmm) cc_final: 0.7764 (mmm) REVERT: C 284 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8442 (mtpt) REVERT: C 286 ASP cc_start: 0.8529 (t70) cc_final: 0.8322 (t70) REVERT: C 289 ILE cc_start: 0.8069 (mp) cc_final: 0.7538 (mm) REVERT: C 294 TYR cc_start: 0.8012 (m-80) cc_final: 0.7539 (m-80) REVERT: C 296 ASN cc_start: 0.7346 (p0) cc_final: 0.6748 (p0) REVERT: C 305 MET cc_start: 0.7133 (mmm) cc_final: 0.6896 (mmm) REVERT: C 313 MET cc_start: 0.8139 (tpp) cc_final: 0.7133 (tpp) REVERT: C 314 GLN cc_start: 0.8519 (tt0) cc_final: 0.8201 (mt0) REVERT: C 316 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 317 ILE cc_start: 0.8793 (mm) cc_final: 0.8222 (mm) REVERT: C 328 LYS cc_start: 0.8332 (mttp) cc_final: 0.8055 (mttp) REVERT: C 340 TRP cc_start: 0.6814 (t60) cc_final: 0.6484 (t60) REVERT: C 361 GLU cc_start: 0.8624 (tp30) cc_final: 0.8164 (tm-30) REVERT: C 371 HIS cc_start: 0.7597 (m170) cc_final: 0.7164 (m-70) REVERT: D 24 ASP cc_start: 0.6702 (t0) cc_final: 0.6377 (t0) REVERT: D 34 ILE cc_start: 0.8127 (mt) cc_final: 0.7658 (mt) REVERT: D 41 GLN cc_start: 0.8009 (tp40) cc_final: 0.7629 (tm-30) REVERT: D 43 VAL cc_start: 0.8486 (m) cc_final: 0.8255 (p) REVERT: D 62 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7332 (mtm-85) REVERT: D 65 LEU cc_start: 0.8490 (mm) cc_final: 0.8173 (mm) REVERT: D 81 ASP cc_start: 0.8162 (m-30) cc_final: 0.7372 (m-30) REVERT: D 84 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8545 (mtmt) REVERT: D 88 HIS cc_start: 0.8615 (t70) cc_final: 0.8354 (t-90) REVERT: D 91 TYR cc_start: 0.8352 (m-80) cc_final: 0.7128 (m-80) REVERT: D 92 ASN cc_start: 0.8056 (m110) cc_final: 0.7609 (m110) REVERT: D 116 ARG cc_start: 0.8207 (mmp-170) cc_final: 0.7579 (mmp-170) REVERT: D 119 MET cc_start: 0.8843 (ttm) cc_final: 0.7905 (ttm) REVERT: D 121 GLN cc_start: 0.8811 (pp30) cc_final: 0.8497 (pp30) REVERT: D 124 PHE cc_start: 0.8037 (m-80) cc_final: 0.7473 (m-80) REVERT: D 137 GLN cc_start: 0.8152 (mt0) cc_final: 0.7905 (mt0) REVERT: D 147 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7170 (mmm160) REVERT: D 175 ILE cc_start: 0.8528 (pt) cc_final: 0.7881 (pt) REVERT: D 176 MET cc_start: 0.7054 (mmm) cc_final: 0.6770 (mmm) REVERT: D 187 ASP cc_start: 0.8744 (m-30) cc_final: 0.8526 (m-30) REVERT: D 192 ILE cc_start: 0.8342 (tp) cc_final: 0.8000 (tp) REVERT: D 203 THR cc_start: 0.8070 (p) cc_final: 0.7316 (p) REVERT: D 207 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7136 (mm-30) REVERT: D 210 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7764 (ttp80) REVERT: D 211 ASP cc_start: 0.8507 (m-30) cc_final: 0.8093 (m-30) REVERT: D 213 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8526 (ttpt) REVERT: D 215 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8769 (mmmt) REVERT: D 216 LEU cc_start: 0.7933 (mm) cc_final: 0.7703 (mm) REVERT: D 240 TYR cc_start: 0.7769 (t80) cc_final: 0.7310 (t80) REVERT: D 254 ARG cc_start: 0.7722 (ptm160) cc_final: 0.7267 (ttp-170) REVERT: D 259 GLU cc_start: 0.8302 (tp30) cc_final: 0.7833 (tp30) REVERT: D 263 GLN cc_start: 0.8604 (mt0) cc_final: 0.8109 (tt0) REVERT: D 276 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 279 TYR cc_start: 0.8039 (t80) cc_final: 0.7544 (t80) REVERT: D 283 MET cc_start: 0.8587 (mmp) cc_final: 0.8130 (mmp) REVERT: D 286 ASP cc_start: 0.8221 (t0) cc_final: 0.7558 (t0) REVERT: D 288 ASP cc_start: 0.8297 (m-30) cc_final: 0.7638 (m-30) REVERT: D 289 ILE cc_start: 0.8189 (pt) cc_final: 0.7485 (mt) REVERT: D 290 ARG cc_start: 0.8047 (mtt180) cc_final: 0.6945 (mtt90) REVERT: D 292 ASP cc_start: 0.8627 (m-30) cc_final: 0.7537 (t0) REVERT: D 293 LEU cc_start: 0.8976 (mt) cc_final: 0.8460 (mt) REVERT: D 294 TYR cc_start: 0.8459 (m-80) cc_final: 0.7842 (m-80) REVERT: D 297 ASN cc_start: 0.8111 (m-40) cc_final: 0.7847 (m-40) REVERT: D 298 VAL cc_start: 0.8379 (t) cc_final: 0.8036 (t) REVERT: D 299 MET cc_start: 0.7952 (mmm) cc_final: 0.7743 (mmm) REVERT: D 305 MET cc_start: 0.7189 (mmp) cc_final: 0.6842 (mmm) REVERT: D 309 ILE cc_start: 0.8742 (pt) cc_final: 0.8356 (pt) REVERT: D 314 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8752 (mm110) REVERT: D 316 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8530 (pt0) REVERT: D 320 LEU cc_start: 0.8834 (mt) cc_final: 0.8456 (mt) REVERT: D 329 ILE cc_start: 0.8295 (mm) cc_final: 0.8002 (mm) REVERT: D 346 LEU cc_start: 0.8197 (tp) cc_final: 0.7906 (tp) REVERT: D 371 HIS cc_start: 0.7620 (p90) cc_final: 0.7177 (p90) outliers start: 0 outliers final: 0 residues processed: 759 average time/residue: 0.3363 time to fit residues: 352.2815 Evaluate side-chains 735 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 735 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 133 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 128 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.113283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087164 restraints weight = 42243.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090971 restraints weight = 25216.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093664 restraints weight = 16998.827| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.8208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15177 Z= 0.204 Angle : 0.726 10.817 20547 Z= 0.367 Chirality : 0.046 0.207 2251 Planarity : 0.005 0.060 2631 Dihedral : 8.971 177.997 2071 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1847 helix: 0.66 (0.18), residues: 844 sheet: -0.79 (0.30), residues: 282 loop : -0.30 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 79 HIS 0.012 0.001 HIS B 41 PHE 0.018 0.001 PHE B 125 TYR 0.042 0.002 TYR A 528 ARG 0.011 0.001 ARG A 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7045.56 seconds wall clock time: 126 minutes 29.36 seconds (7589.36 seconds total)